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 / PHI548 Biomedical Ontology or PHI549 Applied Ontology (can be waived if the student has enrolled in a suitable mentored research tutorial (BMI510 / PHI599) with Ceusters or Smith).

• 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 course will also provide an in-depth review of current research underlying the development of biomedical ontologies as well as a comparative critical analysis of the major current biomedical ontologies and of the methods and tools used in their application, development 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 and maintain our biomedical data, information and 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 and knowledge as well as a critical comparative analysis of the major current biomedical ontologies used in health care and biomedical research settings.

Term paper deadlines

The course concludes with a series of presentations by class participants of their term papers, which should be on a topic in biomedical ontology related to the subject-matter of their PhD research. Relevant deadlines are as follows:

September 7: Selection of term paper topic
October 12: Submission of 300-400 word abstract.
November 9: Submission of draft of term paper.
November 16: Submission of draft of powerpoint presentation.

August 31: Systems and techniques for representing biomedical data, information and knowledge using ontologies (WC)

SLO (Student Learning Outcomes) 4, 5


Advance reading

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 5 (Optional extra session): Core Competency Lectures (WC)

Venue: CTRC 5019A&B
5:00-6:30pm: How to use ontology to analyze a domain.
6:30-8:00pm: Structure of Research Data Files (How to do it Right and Wrong)

September 7: Best practice principles for building ontologies. Introduction to Basic Formal Ontology (BFO) (BS)


Topics discussed

Principles for building ontologies
Principles for defining ontology terms
Introduction to BFO (Part 1)
Discussion of a proposal to define 'capability' within the BFO framework
Today is the deadline for selection of the topic of your term paper.

Advance reading

Barry Smith and Werner Ceusters, “Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies”, Applied Ontology, 5 (2010), 139–188.
Arp R, Smith B, Spear AD. Building Ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 3-4.

September 14: Information Artifact Ontology (IAO) and Ontology for General Medical Science (OGMS) (BS)


Advance reading

Arp R, Smith B, Spear AD. Building Ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 5-6.
Scheuermann RH, Ceusters W, Smith B. "Toward an ontological treatment of disease and diagnosis," Summit Transl Bioinform, 2009 Mar 1;2009:116-20.

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


Advance preparation

Before class, please download the Protégé Ontology Editor and install it locally on your laptop. Bring your laptop to class with you.

Advance reading

Protégé User Guide

After-class exercise

Implement in Protégé terms and definitions from Scheuermann et al. (Due date: September 26.)

September 28: The OBO Foundry (BS)


This session will include a review of the after-class exercises submitted on September 26.

Advance reading Barry Smith, et al., “The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology, 25 (11), November 2007, 1251-1255. PMC2814061

October 3 (Optional extra session): Core Competency Lectures

Venue: CTRC 5019A&B
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

Advance reading

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).

After-class exercise

Read Alert fatigue and propose terms and definitions which need to be added to OGMS to create an ontology to address alert fatigue in EHRs. Due date: October 11

October 12: Building an ontology (WC)


Team exercise

Class participants will be divided into groups. The task for each group will be
1. to identify some area in which ontology methods can be of value in understanding issues related to patient well-being, along the lines illustrated in the advance readings by Ceusters et al., and Souvignet et al. listed below.
2. to propose terms and definitions which need to be added to OGMS to create a corresponding ontology.
3. to make the results available electronically by the end of class.

Today is the deadline for submission of 300-400 word abstracts of your term paper. These abstracts will be critically reviewed in the meeting on October 19.

Advance readings

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 17 (Optional extra session): Core Competency Lecture

Venue: CTRC 5019A&B
5:00-6:30pm: Data Ethics and Responsible Data Sharing (BS)

October 19: Review of term-paper abstracts (WC, BS)

SLO 3, 7

Class participants will be divided into groups. Each group will review critically the 300-400 word abstracts received from the members of other groups on or before October 12. At the end of today's meeting they will present their results in the style of a journal peer review, including where necessary a statement of majority and minority opinions.

October 26 Principles for ontology change management in biomedical information systems (WC)


Advance readings

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

After-class exercise

Correct and improve the results of the exercises described under Sep. 21, Oct. 5 and Oct. 12 above, adhering to the principles of change management outlined on Oct. 26, and taking into account the representation here.

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

SLO 4, 5, 7

Advance reading:

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 post-lecture assignment from Oct. 12 can be used to facilitate combining healthcare data in big data repositories.

November 9 Team exercise: use OGMS to improve biomedical informatics resources (WC, BS)

SLO 3, 7

Advance reading: OMOP

J. Blaisure and W. Ceusters, Improving Common Data Models ‘Fitness for Purpose’ by the Application of Realism Based Ontology
Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)

Advance Reading: RDoC

W. Ceusters, M. Jensen and A. D> Diehl Ontological Realism for the Research Domain Criteria for Mental Disorders
M. Jensen and A. D. Diehl, Integrating an ontology for RDOC with existing biomedical ontologies
Research Domain Criteria (RDoC)

Today is the deadline for submission of the draft of your term paper.

November 16 Evaluation of ontologies (WC, BS)

SLO 4, 6, 8

Advance reading

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.


November 30 Student presentations 1

SLO 6, 7

December 7 Student presentations 2

SLO 1, 4