Advanced Biomedical Ontology: Difference between revisions
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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. | 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'' | ''Course Organization'' | ||
| Line 34: | Line 33: | ||
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. | 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. | ||
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==August 31: Mainstream systems and techniques for modeling, representing and maintaining biomedical data, information and knowledge in ontologies (WC)== | ==August 31: Mainstream systems and techniques for modeling, representing and maintaining biomedical data, information and knowledge in ontologies (WC)== | ||
:SLO 4, 5 | :SLO 4, 5 | ||
| Line 43: | Line 40: | ||
:Yu, A.C., "Methods in Biomedical Ontology", ''Journal of Biomedical Informatics'' 39 (2006) 252–266. | :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 | :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 | ||
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==September 7: Best practice principles for building domain ontologies, terms, and definitions (BS)== | ==September 7: Best practice principles for building domain ontologies, terms, and definitions (BS)== | ||
| Line 48: | Line 47: | ||
: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. | ||
---- | |||
==September 14: Basic Formal Ontology (BS)== | ==September 14: Basic Formal Ontology (BS)== | ||
| Line 53: | Line 54: | ||
: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. | ||
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==September 21: Introduction to Protégé ontology editor and add-on tools (Neil Otte)== | ==September 21: Introduction to Protégé ontology editor and add-on tools (Neil Otte)== | ||
| Line 60: | Line 63: | ||
:Exercise: Implement in Protégé terms and definitions from the September 14 assignment. Due date: October 17. | :Exercise: Implement in Protégé terms and definitions from the September 14 assignment. Due date: October 17. | ||
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==September 28: The Ontology of General Medical Science (OGMS) (BS) | ==September 28: The Ontology of General Medical Science (OGMS) (BS) | ||
| Line 73: | Line 78: | ||
:Assignment post-lecture: Read [https://psnet.ahrq.gov/primers/primer/28/alert-fatigue Alert fatigue] and expand the OGMS with terms and definitions required for an ontology to address alert fatigue in EHRs. Due date: October 11 | :Assignment post-lecture: Read [https://psnet.ahrq.gov/primers/primer/28/alert-fatigue Alert fatigue] and expand the OGMS with terms and definitions required for an ontology to address alert fatigue in EHRs. Due date: October 11 | ||
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==October 12: Team exercise: building an ontology for patient safety (WC)== | ==October 12: Team exercise: building an ontology for patient safety (WC)== | ||
| Line 79: | Line 86: | ||
: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. | :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 | :Souvignet J, Rodrigues JM. Toward a patient safety upper level ontology. Stud Health Technol Inform. 2015;210:160-4. Team exercise | ||
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==October 19: Ontology of food, health and physical activity (BS)== | ==October 19: Ontology of food, health and physical activity (BS)== | ||
| Line 84: | Line 93: | ||
:READINGS TO BE SUPPLIED | :READINGS TO BE SUPPLIED | ||
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==October 26 Principles for change management in ontologies and for upgrading to new ontologies in biomedical information system (WC)== | ==October 26 Principles for change management in ontologies and for upgrading to new ontologies in biomedical information system (WC)== | ||
| Line 91: | Line 102: | ||
: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 | :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 | ||
W10 | W10 | ||
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==November 2 Ontological principles for combining healthcare data in big data repositories (WC+BS)== | |||
:SLO 4,5,7 | |||
:Ceusters W, Hsu CY, Smith B. "[http://www.referent-tracking.com/RTU/sendfile/?file=ICBO2014-CeustersHsuSmith-FinalCameraReady.pdf 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 | 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 | SLO 3, 7 | ||
Observational Medical Outcomes Partnership Common Data Model (http://omop.org/CDM) | Observational Medical Outcomes Partnership Common Data Model (http://omop.org/CDM) | ||
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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. | 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. | ||
FALL RECESS | |||
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FALL RECESS | |||
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W13 Nov 30 6, 7 WC+BS Student presentations: critical review of biomedical ontology papers To be supplied | 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 | W14 Dec 7 1,4 WC+BS Student presentations: critical review of biomedical ontology papers To be supplied | ||
Revision as of 21:19, 28 May 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 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)
- SLO 1
- 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 of 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 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)
- SLO 7
- 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
- READINGS TO BE SUPPLIED
October 26 Principles for change management in ontologies and for upgrading to new ontologies in biomedical information system (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
- 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
W10
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 (http://omop.org/CDM)
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.
FALL RECESS
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
