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Course Title: Advanced Topics in Biomedical Ontology
==Background Information==


Cross-listed: Department of Biomedical Informatics (BMI 708 SEM) and Department of Philosophy (PHI 637 SEM)
'''Department of Biomedical Informatics and Department of Philosophy'''


Course Subject Code:
:Type of Instruction: Seminar


Course Number:
:BMI 708 SEM, PHI 637 SEM


Type of Instruction:
:Semester: Fall 2017


Class Number:
• Thursday: 4pm to 6:50pm


Semester:
• 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: [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters, MD]. Contact: 77 Goodell Street, 5th floor, by
 
appointment only through wceusters@gmail.com
 
:Philosophy: [http://ontology.buffalo.edu/smith/ 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 ([http://ncor.buffalo.edu/2017/SLO.htm Student Learning Outcomes]) 4, 5
 
[https://buffalo.box.com/s/tb03t4x1e3snhcmmnnewbb1pakvwptnc Slides]
 
[https://buffalo.box.com/s/7me3csuyy0d1bh6g5ivnu8v6zfpy26ts Video]
 
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.
: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
 
----
 
==September 5 (Optional extra session): Core Competency Lectures (WC)==
5:00-6:30pm: How to use ontology to analyze a domain. [http://www.referent-tracking.com/RTU/files/CTSI-CCL-BMI-class1-ontology_for_domain_analysis.pptx Slides]
 
6:30-8:00pm: Structure of Research Data Files (How to do it Right and Wrong) [http://www.referent-tracking.com/RTU/files/CTSI-CCL-BMI-class1-research-data-files.pptx Slides]
 
----
 
==September 7: Best practice principles for building ontologies. Introduction to Basic Formal Ontology (BFO) (BS)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 1
 
[https://buffalo.box.com/s/nhl627625mv23sih6642mifztkx26166 Slides]


BMI
[https://buffalo.box.com/s/nib5z762bca93crzxm72rlq2syu4ee21 Video]


708
: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


SEM
::[https://www.youtube.com/watch?v=gJxfZ3cq5jE Video on functions, dispositions and capabilities]


to be assigned
:Today is the deadline for selection of the '''topic''' of your term paper.


Fall of odd years
Advance reading
:[https://www.researchgate.net/profile/Barry_Smith4/publication/51188119_Ontological_realism_A_methodology_for_coordinated_evolution_of_scientific_ontologies/links/02e7e52e910d23b28b000000/Ontological-realism-A-methodology-for-coordinated-evolution-of-scientific-ontologies.pdf 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.
----


PHI
==September 14: [http://www.obofoundry.org/ontology/iao.html Information Artifact Ontology] (IAO) and [http://www.obofoundry.org/ontology/ogms.html Ontology for General Medical Science] (OGMS) (BS) ==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 2


TBD
[https://buffalo.box.com/s/z72w55bzgs5tlyxw7je1unvrqyof9hu2 Slides]


SEM
[https://buffalo.box.com/s/5dugfsnskqpdp383e1ksdchslxyrz30f Video]


to be assigned
:Introduction to BFO (Part 2)
:Introduction to IAO
:Introduction to OGMS


Fall of odd years
Advance reading


1. Course Information
:Arp R, Smith B, Spear AD. ''Building Ontologies with Basic Formal Ontology''. MIT Press, 2015, chapters 5-6.


• Date(s)/Time(s): to be assigned
:[http://ceur-ws.org/Vol-1515/regular10.pdf Aboutness: W. Ceusters, B. Smith, "Towards Foundations for the Information Artifact Ontology"]


• Delivery Mode: Traditional
: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.


• Number of Credits: 3
----
 
==September 21: Protégé Quickstart for Users of BFO ([http://www.jneilotte.com/ Neil Otte])==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 7
 
[https://buffalo.box.com/s/irx9zdg1fq0w5iw7u5lxjzjgyukwv902 Slides]
 
[https://buffalo.box.com/s/d4tl6v1w2hpdpg6yhyr5ia510mru7qqx Video]
 
[https://buffalo.box.com/s/hoo3bk43eanf1rzk5kf1s5b4eckrqakg Class Exercise]
 
[https://buffalo.box.com/s/vjdx999434t3ncga1lagzxi2ueicganx Class Exercise (OWL)]
 
Advance preparation
:Before class, please download the [http://protege.stanford.edu/ Protégé Ontology Editor] and install it locally on your laptop. Bring your laptop to class with you.
 
Advance reading
:[https://protegewiki.stanford.edu/wiki/Pr4_UG Protégé User Guide]
 
After-class exercise
:Implement in Protégé terms and definitions from [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 Scheuermann et al]. (Due date: September 26.)
----
 
==September 28: The OBO Foundry (BS)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 3
 
[https://buffalo.box.com/s/bh4dzvbvelonsne0devwxadw0qys1m8e Slides]
 
This session will include a review of the after-class exercises submitted on September 26.
 
Advance reading
Barry Smith, et al., “[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf 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: [http://www.buffaloctrc.org/contact/ CTRC 5019A&B]
:5:00pm: How to Write Grants (BS) [https://buffalo.box.com/s/7mp8lgh2s45cxhfp5m0iqhhqxpyvi16z Slides]
:6:30pm: How to Get published (BS) [https://buffalo.box.com/s/4n05d7jy7i5a7n2cr3mvdvlkq6qeomas Slides]
----
 
==October 5: Using referent tracking for building ontologies (WC)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 1, 2, 4, 6
 
[https://buffalo.box.com/s/vk8y8d2h7o7dk0bs3ijjbew0y8fxmbay Slides]
 
[https://buffalo.box.com/s/qvoet8xfxx7qigpy8oq6kur6eudm7lqd Video]
 
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 [https://psnet.ahrq.gov/primers/primer/28/alert-fatigue 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==
[http://ncor.buffalo.edu/2017/SLO.htm 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. "[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.
:Souvignet J, Rodrigues JM. "[http://ebooks.iospress.nl/publication/39316 Toward a patient safety upper level ontology]," ''Stud Health Technol Inform''. 2015;210:160-4.
----
 
==October 17 (Optional extra session): Core Competency Lecture==
:Venue: [http://www.buffaloctrc.org/contact/ CTRC 5019A&B]
:5:00-6:30pm: Data Ethics and Responsible Data Sharing (BS) [https://buffalo.box.com/s/b9yk8ma7rd3cwf0u6nd4le7pcdsf80gy Slides]
----
 
==October 19: Review of term-paper abstracts (WC, BS)==
[http://ncor.buffalo.edu/2017/SLO.htm 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:'''
 
[https://buffalo.box.com/s/mkp3tvihs4xp8en4w6bsk9fx4e9mdxjz Blaisure]: Ontological Study of Temporal Entities and Temporal Relations in Common Data Models
 
[https://buffalo.box.com/s/2honlhznv9wcze4qgzvetixp84vt6fia Cox]: OGMS 2.0 – A Proposed Improvement and Extension ofthe Ontology for General Medical Science
 
[https://buffalo.box.com/s/a8y10cph71pjod2vd12lfu0bk7i6gbqz Davies]: Ontology for National Quality Forum Evaluation Forms
 
[https://buffalo.box.com/s/oecmliaoqfkl7n0ln6zfiblvk6exuzwv Jensen]: Linking Mental Disorders to Research Domain Criteria Constructs via OGMS and the Mental Disease Ontology
 
[https://buffalo.box.com/s/8f4rdq7agykc1gpz21jb0v1rl4fd4bv1 Mammen]: Adverse Events and Compound Interactions
 
'''Group 2:'''
 
[https://buffalo.box.com/s/6ptkkcx58z7nnlckumo22a9cyj2c2nud Hudson]: Ontology for the Computational Analysis of Novel Drug Opportunities
 
[https://buffalo.box.com/s/d1nfu14y6i2rd6tmva62dnn752jkiov2 Mullin]: Ontology-Based Classifier for Diseases
 
[https://buffalo.box.com/s/pqshxtu5k8wfv5f1rrnmlv3l8p8e6s4p Schuler]: Diabetes Ontology
 
[https://buffalo.box.com/s/t5079dh5yamnpqnlcafpo88xrigb8zcx Shyamashree Sinha]: Evaluating the Ontology of Epidemics
 
[https://buffalo.box.com/s/b60ouwn1fykv17zn96jsv86hq2pbllvs Serra]: Cancer Cell Ontology
 
[https://buffalo.box.com/s/vela25trscbc81klol3zs6iuoplgv3eu Zhao]: Ontology of Trauma Surgery
 
----
 
==October 26 Principles for ontology change management in biomedical information systems (WC)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO]
 
[https://buffalo.box.com/s/98mk9zclp45kzap96f17bujs1biz920d Slides]
 
[https://buffalo.box.com/s/ju5eh12uhaakv17nve5vlywadcjv8i69 Video]
 
Advance readings
:Ceusters W. "[http://ac.els-cdn.com/S1532046408001524/1-s2.0-S1532046408001524-main.pdf?_tid=1a2ec366-590a-11e7-83a5-00000aab0f6b&acdnat=1498328738_e3e5f4489fac161dba5c12d2ad919e39 Applying Evolutionary Terminology Auditing to the Gene Ontology]", ''Journal of Biomedical Informatics'' 2009;42:518–529.
:Ceusters W. "[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243179/ 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 [http://www.ontobee.org/ontology/OGMS here].
----
 
==November 2 Ontological principles for combining healthcare data in big data repositories (WC,BS)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 4, 5, 7
 
[https://buffalo.box.com/s/gie67giz1wem0hgqk9arb0wydagjjpi7 Slides1]
 
[https://buffalo.box.com/s/zwqs9b5v934iyikxmgxsna7q04bdxvue Slides2]
 
[https://buffalo.box.com/s/jg4thkz0n8aqkpp87fy41qqlbs20vq9u Video]
 
Advance readings:
 
:Gliklich RE, et al. [https://www.ncbi.nlm.nih.gov/books/NBK208625/ "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. "[http://www.referent-tracking.com/RTU/files/ICBO2014-CeustersHsuSmith-FinalCameraReady/1.0/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 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)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 3, 7
 
'''Advance reading: OMOP'''
 
:[https://buffalo.box.com/s/hypd36e8msxr0u2bi8g5gndos8afbl9t J. Blaisure and W. Ceusters, Improving Common Data Models ‘Fitness for Purpose’ by the Application of Realism Based Ontology]


• Instructors
:[http://omop.org/CDM Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)]


Course directors: Biomedical Informatics: Werner Ceusters, MD (contact: 77 Goodell Street, 5th floor, by
'''Advance Reading: RDoC'''


appointment only through wceusters@gmail.com)
:[https://buffalo.box.com/s/o33sbscswbc0u64yj47y74a4za04lfsc W. Ceusters, M. Jensen and A. D. Diehl, Ontological Realism for the Research Domain Criteria for Mental Disorders]


Philosophy: Barry Smith, PhD (contact: 126 Park Hall, N Campus, by appointment only through
:[https://buffalo.box.com/s/fo6sf1wyudlug5prhtb4aefljhwlsyy4 M. Jensen and A. D. Diehl, Integrating an ontology for RDOC with existing biomedical ontologies]


phismith@buffalo.edu)
:[https://gopher.nimh.nih.gov/research-priorities/rdoc/index.shtml Research Domain Criteria (RDoC)]


Lecturers: Werner Ceusters and Barry Smith
Today is the deadline for submission of the draft of your term paper.
----


2. Course Description
==November 16 Evaluation of ontologies (WC, BS)==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 4, 6, 8


The course begins with a review of the theories underlying biomedical knowledge representation and ontology. The methods
Barry Smith: The Evaluation of Ontologies


and tools for applied ontology as well as the management and maintenance of biomedical ontologies will be discussed in
[https://buffalo.box.com/s/zbvva3cdrolurqtkybuzv12rs72pvs9y Slides 1] 


detail including the principles of ontological realism and the implementation thereof in the Basic Formal Ontology (BFO).
[https://buffalo.box.com/s/6ojm7gm7n1o58zjqf0gsa7uo6pq6qqb7 Video 1]


Students will gain experience with the Web Ontology Language (OWL) and the limitations thereof, and with utilities to
Werner Ceusters: Evolutionary Quality Assessment of Ontologies


query ontologies expressed in OWL. The students will learn how to use and evaluate classifiers and their role in
[http://www.referent-tracking.com/RTU/files/BMI708-20171026-Class12-OntologyEvaluation.pptx Slides 2]


subsumption. They will learn both the transitive and reflexive closure of subsumption and its applied use in ontology
[https://buffalo.box.com/s/h96gjcsyu9ahwmb3phpaazz4of77v7y5 Video 2]


development, maintenance and use. This course also provides an in-depth review of current theories and research underlying
Advance reading
:Barry Smith, “[http://ontology.buffalo.edu/smith/articles/Ontology(Science).pdf 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. "[http://ontology.buffalo.edu/smith/articles/evaluationofontologies.pdf 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
----


the development of biomedical ontologies as well as a comparative critical analysis of the major current biomedical
==November 30 Student presentations 1==
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 6, 7


ontologies as well as the methods and tools for biomedical ontology development, use and evaluation.
4:05p.m. Jonathan Blaisure: Ontological Study of Temporal Entities and Temporal Relations in Common Data Models [https://buffalo.box.com/s/sb4l09m44x7kv4vnk787p13kscjuw86w Slides]


• Course prerequisites: BMI508 or PHI548 or PHI549.
4:30p.m. Sheryl Davies: Reliability, Signal, Population and Purpose [https://buffalo.box.com/s/t985zficevgmi4dyip5fiaz5ihca10wy Slides]


5:00p.m. Sarah Mullin: Ontology-Based Classifier for Diseases


9. Course Organization / Schedule
5:30pm Break
Reference: http://registrar.buffalo.edu/calendars/academic/


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.
5:35 Manoj Mammen: Adverse Events and Compound Interactions


Week
6:05 Alexander Cox: Diagnosing Alzheimer's Disease [https://buffalo.box.com/s/cc8orrafaijry0zjgdywwp1xxwh8xatu Slides]
2017 SLO Instr. Topic Required readings prior to lecture Assignment post-lecture Due Date
==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)==
==December 7 Student presentations 2==
SLO 1
[http://ncor.buffalo.edu/2017/SLO.htm SLO] 1, 4


:Arp R, Smith B, Spear AD. Building ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 3-4.
4:05pm Matt Hudson: Ontology for the Computational Analysis of Novel Drug Opportunities [https://buffalo.box.com/s/8w8him0x49encw2spdhot6r7q3itqvdq Slides]


==September 14, Basic Formal Ontology (BS)
4:30pm Jim Schuler: Diabetes Ontology [https://buffalo.box.com/s/4z675tvseu3g3uqwanl1klcr3imibsh2 Slides]
SLO 2


:Arp R, Smith B, Spear AD. Building ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 5-6.
5:00pm Shyamashree Sinha: Evaluating the Ontology of Epidemics [https://buffalo.box.com/s/8w8him0x49encw2spdhot6r7q3itqvdq Slides]
SLO 2


==September 21, Introduction to Protégé ontology editor and add-on tools (Neil Otte)==
5:25pm Break


:Web Protégé User Guide (http://protegewiki.stanford.edu/wiki/WebProtegeUsersGuide)
5:30pm Luc Serra: Cancer Cell Ontology [https://buffalo.box.com/s/dwlfb4pi5v7xsthvcrkzz2w2j48pkokp Slides]
SLO 7
Implement terms and definitions from the W5 assignment in Protégé.
2 days prior to W8
W5 Sep 28
3 BS The Ontology of General Medical Science (OGMS) Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit Transl Bioinform. 2009 Mar 1;2009:116-20.
W6 Oct 5
1, 2, 4, 6 WC Using referent tracking for building ontologies 1) Arp R, Smith B, Spear AD. Building ontologies with Basic Formal Ontology. MIT Press, 2015, chapter 7.
2) Hogan WR and Ceusters W. Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis. Journal of Biomedical Semantics 2016;7(54). Read AHRQ’s ‘Alert fatigue’ article (https://psnet.ahrq.gov/primers/primer/28/alert-fatigue). Expand the OGMS with terms and definitions required for an ontology to address alert fatigue in EHRs. Prior to
W7


W7 Oct 12 7 WC Team exercise: building an ontology for patient safety 1) 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.
5:55pm Jane Zhao: Ontology of Trauma Surgery [https://buffalo.box.com/s/rvk9jza7qqsbn0k0o26k9r3t04hnkz72 Slides]
2) Souvignet J, Rodrigues JM. Toward a patient safety upper level ontology. Stud Health Technol Inform. 2015;210:160-4. Team exercise
W8 Oct 19 3, 7 BS Ontology of health and physical activity To be supplied
W9
Oct 26 8 WC Principles for change management in ontologies and for upgrading to new ontologies in biomedical information systems 1) Ceusters W. Applying Evolutionary Terminology Auditing to the Gene Ontology. Journal of Biomedical Informatics 2009;42:518–529.
2) Ceusters W. SNOMED CT Revisions and Coded Data Repositories: When to Upgrade? In American Medical Informatics Association 2011 Annual Symposium Proceedings, Washington DC, October 22-26, 2011:197-206 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. Prior to W11
W10 Nov 2 4,5,7 WC+BS Ontological principles for combining healthcare data in big data repositories Ceusters W, Hsu CY, Smith B. Clinical Data Wrangling using Ontological Realism and Referent Tracking. International Conference on Biomedical Ontologies, ICBO 2014, Houston, Texas, Oct 6-9, 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 3, 7 WC+BS Team exercise: using the OGMS to improve the OMOP, case reports, guidelines, or course of illness systems 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

Latest revision as of 16:04, 11 December 2017

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

Slides

Video

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

Slides

Video

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
Video on functions, dispositions and capabilities
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

Slides

Video

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.
Aboutness: W. Ceusters, B. Smith, "Towards Foundations for the Information Artifact Ontology"
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

Slides

Video

Class Exercise

Class Exercise (OWL)

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)

SLO 3

Slides

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

Slides

Video

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

Slides

Video

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

Slides1

Slides2

Video

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

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

Barry Smith: The Evaluation of Ontologies

Slides 1

Video 1

Werner Ceusters: Evolutionary Quality Assessment of Ontologies

Slides 2

Video 2

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 Slides

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

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