Advanced Biomedical Ontology: Difference between revisions
From NCOR Wiki
Jump to navigationJump to search
mNo edit summary |
mNo edit summary |
||
| Line 27: | Line 27: | ||
'''Course Description''' | '''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 | 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'' | ''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 | 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. | ||
---- | ---- | ||
| Line 38: | Line 38: | ||
:SLO ([http://ncor.buffalo.edu/2017/SLO.htm Student Learning Outcomes]) 4, 5 | :SLO ([http://ncor.buffalo.edu/2017/SLO.htm Student Learning Outcomes]) 4, 5 | ||
Advance reading: | |||
:Yu, A.C., "[http://www.sciencedirect.com/science/article/pii/S1532046405001310?via%3DihubMethods in Biomedical Ontology]", ''Journal of Biomedical Informatics'' 39 (2006) 252–266. | :Yu, A.C., "[http://www.sciencedirect.com/science/article/pii/S1532046405001310?via%3DihubMethods in Biomedical Ontology]", ''Journal of Biomedical Informatics'' 39 (2006) 252–266. | ||
:Robert Hoehndorf, Paul N. Schofield and Georgios V. Gkoutos, "[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652617/ The role of ontologies in biological and biomedical research: a functional perspective]", ''Briefings in Bioinformatics'', 2015, 1–12 | :Robert Hoehndorf, Paul N. Schofield and Georgios V. Gkoutos, "[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652617/ The role of ontologies in biological and biomedical research: a functional perspective]", ''Briefings in Bioinformatics'', 2015, 1–12 | ||
| Line 46: | Line 47: | ||
:[http://ncor.buffalo.edu/2017/SLO.htm SLO] 1 | :[http://ncor.buffalo.edu/2017/SLO.htm SLO] 1 | ||
: | :Today is the deadline for selection of the '''topic''' for your term papers to be presented at the end of the semester. (Deadline for submission of 300-400 word abstracts is October 12.) The topic can be any aspect of biomedical ontology research (including where relevant topics related to your PhD research). | ||
Advance reading: | |||
:Arp R, Smith B, Spear AD. ''Building Ontologies with Basic Formal Ontology''. MIT Press, 2015, chapters 3-4. | :Arp R, Smith B, Spear AD. ''Building Ontologies with Basic Formal Ontology''. MIT Press, 2015, chapters 3-4. | ||
| Line 55: | Line 57: | ||
:[http://ncor.buffalo.edu/2017/SLO.htm SLO] 2 | :[http://ncor.buffalo.edu/2017/SLO.htm SLO] 2 | ||
Advance reading: | |||
:Arp R, Smith B, Spear AD. ''Building Ontologies with Basic Formal Ontology''. MIT Press, 2015, chapters 5-6. | :Arp R, Smith B, Spear AD. ''Building Ontologies with Basic Formal Ontology''. MIT Press, 2015, chapters 5-6. | ||
| Line 64: | Line 67: | ||
:[http://protegewiki.stanford.edu/wiki/WebProtegeUsersGuide Web Protégé User Guide] | :[http://protegewiki.stanford.edu/wiki/WebProtegeUsersGuide Web Protégé User Guide] | ||
:Exercise: Implement in Protégé terms and definitions from | :Exercise: Implement in Protégé terms and definitions from Scheuermann et al. Due date: October 17. | ||
:Scheuermann RH, Ceusters W, Smith B. "[https://www.researchgate.net/profile/Barry_Smith4/publication/49967856_Toward_an_Ontological_Treatment_of_Disease_and_Diagnosis/links/02e7e52e910d257efd000000/Toward-an-Ontological-Treatment-of-Disease-and-Diagnosis.pdf Toward an ontological treatment of disease and diagnosis]," ''Summit Transl Bioinform'', 2009 Mar 1;2009:116-20. | |||
---- | ---- | ||
| Line 71: | Line 75: | ||
:[http://ncor.buffalo.edu/2017/SLO.htm SLO] 3 | :[http://ncor.buffalo.edu/2017/SLO.htm SLO] 3 | ||
---- | ---- | ||
| Line 92: | Line 96: | ||
:[http://ncor.buffalo.edu/2017/SLO.htm SLO] 7 | :[http://ncor.buffalo.edu/2017/SLO.htm 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 | :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 as concerns issues of patient care and patient safety. | ||
:Today is the deadline for submission of 300-400 word abstracts for . The topic can be any aspect of biomedical ontology research, including, where relevant, topics related to your PhD research. abstracts to be discussed in the meeting on October 19, complete versions of which will be presented in the final class session(s). Th | |||
:Ceusters W, Capolupo M, De Moor G, Devlies J, Smith B. "[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103706/ An Evolutionary Approach to Realism-Based Adverse Event Representations]," ''Methods of Information in Medicine'', 2011;50(1):62-73. | :Ceusters W, Capolupo M, De Moor G, Devlies J, Smith B. "[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103706/ An Evolutionary Approach to Realism-Based Adverse Event Representations]," ''Methods of Information in Medicine'', 2011;50(1):62-73. | ||
Revision as of 13:33, 26 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 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.
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
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 7: Best practice principles for building domain ontologies, terms, and definitions. (BS)
- SLO 1
- Today is the deadline for selection of the topic for your term papers to be presented at the end of the semester. (Deadline for submission of 300-400 word abstracts is October 12.) The topic can be any aspect of biomedical ontology research (including where relevant topics related to your PhD research).
Advance reading:
- 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
Advance reading:
- 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 Scheuermann et al. Due date: October 17.
- Scheuermann RH, Ceusters W, Smith B. "Toward an ontological treatment of disease and diagnosis," Summit Transl Bioinform, 2009 Mar 1;2009:116-20.
September 28: The Ontology for General Medical Science (OGMS) (BS)
- SLO 3
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 as concerns issues of patient care and patient safety.
- Today is the deadline for submission of 300-400 word abstracts for . The topic can be any aspect of biomedical ontology research, including, where relevant, topics related to your PhD research. abstracts to be discussed in the meeting on October 19, complete versions of which will be presented in the final class session(s). Th
- 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
