Advanced Biomedical Ontology
Background Information
Department of Biomedical Informatics and Department of Philosophy
- Type of Instruction: Seminar
- 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 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 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)
5:00-6:30pm: How to use ontology to analyze a domain. Slides
6:30-8:00pm: Structure of Research Data Files (How to do it Right and Wrong) Slides
September 7: Best practice principles for building ontologies. Introduction to Basic Formal Ontology (BFO) (BS)
SLO 1
- 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)
SLO 2
- Introduction to BFO (Part 2)
- Introduction to IAO
- Introduction to OGMS
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: Protégé Quickstart for Users of BFO (Neil Otte)
SLO 7
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
After-class exercise
- Implement in Protégé terms and definitions from Scheuermann et al. (Due date: September 26.)
September 28: The OBO Foundry (BS)
SLO 3
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) Slides
- 6:30pm: How to Get published (BS) Slides
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
SLO 7
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) Slides
October 19: Review of term-paper abstracts (WC, BS)
SLO 3, 7
4pm Students present their abstracts, max 4 minutes each, to be timed.
4:45pm Each group discusses the abstracts of all students NOT in their group. One rapporteur should be selected for each abstract to present conclusions highlighting 1) strengths, 2) weaknesses, 3) threats to successful completion. Presentations should be use roughly 3 powerpoint slides.
5:30pm Each abstract should be reported on by the corresponding rapporteur from the other group. Max 5 minutes per abstract.
Group 1:
Blaisure: Ontological Study of Temporal Entities and Temporal Relations in Common Data Models
Cox: OGMS 2.0 – A Proposed Improvement and Extension ofthe Ontology for General Medical Science
Davies: Ontology for National Quality Forum Evaluation Forms
Jensen: Linking Mental Disorders to Research Domain Criteria Constructs via OGMS and the Mental Disease Ontology
Mammen: Adverse Events and Compound Interactions
Group 2:
Hudson: Ontology for the Computational Analysis of Novel Drug Opportunities
Mullin: Ontology-Based Classifier for Diseases
Schuler: Diabetes Ontology
Shyamashree Sinha: Evaluating the Ontology of Epidemics
Serra: Cancer Cell Ontology
Zhao: Ontology of Trauma Surgery
October 26 Principles for ontology change management in biomedical information systems (WC)
SLO 8
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 readings:
- Gliklich RE, et al. "Interfacing Registries With Electronic Health Records", ch. 15 of Registries for Evaluating Patient Outcomes: A User's Guide, Rockville, MD: Agency for Healthcare Research and Quality, 2014.
- 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
Advance Reading: 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
Barry Smith: The Evaluation of Ontologies
Werner Ceusters: Evolutionary Quality Assessment of Ontologies
Advance reading
- Barry Smith, “Ontology (Science)”, in C. Eschenbach and M. Grüninger (eds.), Formal Ontology in Information Systems. Proceedings of the Fifth International Conference (FOIS 2008), Amsterdam: IOS Press, 21-35.
- 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
4:05p.m. Jonathan Blaisure: Ontological Study of Temporal Entities and Temporal Relations in Common Data Models
4:30p.m. Sheryl Davies: Reliability, Signal, Population and Purpose Slides
5:00p.m. Sarah Mullin: Ontology-Based Classifier for Diseases
5:30pm Break
5:35 Manoj Mammen: Adverse Events and Compound Interactions
6:05 Alexander Cox: Diagnosing Alzheimer's Disease Slides
December 7 Student presentations 2
SLO 1, 4
4:05pm Matt Hudson: Ontology for the Computational Analysis of Novel Drug Opportunities Slides
4:30pm Jim Schuler: Diabetes Ontology Slides
5:00pm Shyamashree Sinha: Evaluating the Ontology of Epidemics Slides
5:25pm Break
5:30pm Luc Serra: Cancer Cell Ontology Slides
5:55pm Jane Zhao: Ontology of Trauma Surgery Slides
