Biomedical Ontology 2016: Difference between revisions

Latest revision as of 11:30, 27 September 2023

PHI 548 (seminar, 3 credits). Registration number: 24057

This course is cross-listed with BMI 508, which is offered as part of the newly accredited PhD program in UB's Department of Biomedical Informatics

Time: 4:00-6:50pm, Mondays, Fall Semester 2016

Room: Baldy 200-G, UB North Campus

Instructors: Barry Smith (Philosophy) and Werner Ceusters (Biomedical Informatics)

Office hours: BS: by appointment via email; WC: TBA

Course Description

This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experiments and through patient care, and show how ontologies are used in accessing, maintaining and exploiting the results. We will describe how biomedical ontologies are developed and evaluated and provide a comparative critical analysis of the principal current ontology resources. We will also review the major theories, methods and tools for the development of ontologies, and illustrate how these are being used in different areas of biomedical research and healthcare. On completion of this course students will have a thorough understanding of strategies to manage and exploit biomedical data; they will have a knowledge of categorization, of the philosophy of experimentation, of the philosophy of medicine, and of computer-based reasoning with data. The seminar will be highly interactive, featuring debates between Drs Smith and Ceusters and between Smith and Ceusters and the course participants.

All slides and videos will be made available at this link

@@ Line 1: / Line 1: @@
-Faculty:
-PHI 548. Cross-listed with BMI 508
+'''PHI 548 (seminar, 3 credits). Registration number: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=24057 24057]'''
+'''This course is cross-listed with BMI 508, which is offered as part of the newly accredited PhD program in UB's [http://www.smbs.buffalo.edu/biomedicalinformatics/index.php Department of Biomedical Informatics]
 '''Time''': 4:00-6:50pm, Mondays, Fall Semester 2016
 '''Room''': Baldy 200-G, UB North Campus
 '''Instructors''': [http://ontology.buffalo.edu/smith/ Barry Smith] (Philosophy) and [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters] (Biomedical Informatics)
-'''Office hours''': BS: Tuesdays, 12:15-1pm in 126 Park Hall and by appointment via email to [mailto:phismith@buffalo.edu]; WC:
+'''Office hours''': BS: by appointment via [mailto:phismith@buffalo.edu email]; WC: TBA
-Credit Hours
+'''Course Description'''
+This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experiments and through patient care, and show how ontologies are used in accessing, maintaining and exploiting the results. We will describe how biomedical ontologies are developed and evaluated and provide a comparative critical analysis of the principal current ontology resources. We will also review the major theories, methods and tools for the development of ontologies, and illustrate how these are being used in different areas of biomedical research and healthcare. On completion of this course students will have a thorough understanding of strategies to manage and exploit biomedical data; they will have a knowledge of categorization, of the philosophy of experimentation, of the philosophy of medicine, and of computer-based reasoning with data. The seminar will be highly interactive, featuring debates between Drs Smith and Ceusters and between Smith and Ceusters and the course participants.
+All slides and videos will be made available at [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology this link]
+=='''Recommended background reading''' ==
+:R. Arp, B. Smith, A. D. Spear, ''[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]''
+== '''Recommended background video content''' ==
+Selections from: [http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013]
 == '''Schedule''' ==
-BMI 508:  Biomedical Ontology  (3 credits)
+== 8/29/2016 Introduction to Ontology 1: General Overview (BS) ==
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-1.pptx Slides]
+Roots of ontology in
+*artificial intelligence ([https://www.academia.edu/722721/The_second_naive_physics_manifesto Second Naive Physics Manifesto])
+*library science ([https://www.nlm.nih.gov/mesh/subhierarchy.html MeSH])
+*Semantic Web ([https://en.wikipedia.org/wiki/Web_Ontology_Language OWL])
+*Human Genome Project ([http://geneontology.org Gene Ontology])
+== 9/12/2016  Ontology of Clinical Practice (WC) ==
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-2.pptx Slides]
+Disease vs. diagnosis; Electronic Health Records and other systems and techniques for modeling, representing and maintaining patient data
+*[http://www.slideserve.com/joben/toward-an-ontology-for-general-medical-science Ontology for General Medical Science]
+*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Toward an Ontological Treatment of Disease and Diagnosis]
+== 9/19/2016  Ontology of Experiments (WC, BS) ==
+'''Part 1: Ontology of Clinical Practice (continued)''' (WC)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-3-part1.pptx Slides]
+Representing clinical data
+'''Part 2: Ontology of Scientific Research''' (BS)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-3-part2.pptx Slides]
+Background on philosophy of science
+The generation and dissemination of new knowledge through scientific experiments
+Biomedical research and clinical trials
+The Information Artifact Ontology
+*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154556 Ontology for Biomedical Investigations (OBI)]
+*[http://ceur-ws.org/Vol-1515/regular10.pdf Information Artifact Ontology]
+*[http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2015;volume=6;issue=1;spage=37;epage=37;aulast=Smith Image Ontologies]
+Video: [https://www.youtube.com/watch?v=booqxkpvJMg Clinical Trial Data Wants to be Free]
+== 9/26/2016  Introduction to Ontology 2: Ontology in Buffalo (BS) ==
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-4.pdf Slides]
+Includes a presentation by [https://scholar.google.com/citations?user=BUcx6agAAAAJ&hl=en Alex Diehl] on the Cell and Protein Ontologies
+*[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]
+*[http://obofoundry.org/ Open Biomedical Ontologies (OBO) Foundry]
+*[http://obofoundry.org/ontology/iao.html Information Artifact Ontology]
+*[http://www.referent-tracking.com/RTU/?page=index Referent Tracking]
+*[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-6 Logical development of the Cell Ontology]
+*[http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0088-7 The Cell Ontology 2016]
+*[http://nar.oxfordjournals.org/content/42/D1/D415.long Protein Ontology: a controlled structured network of protein entities]
+== 10/3/2016  Ontology of Social Entities (BS) ==
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-5.pdf Slides]
+Ontology of obligations
+Speech act theory
+Patient consent
+Healthcare organizations
+*[http://ontology.buffalo.edu/document_ontology/ Document Acts]
+*[http://www.ontobee.org/ontology/d-acts d-acts Ontology]
+== 10/10/2016 How to Build an Ontology (BS/WC/[http://www.jneilotte.com/ NO])==
+Principles of ontology building (BS) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-6-part1.pptx Slides]
+Further principles of ontology building (WC) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-6-part2.pptx Slides]
+First look at [http://protege.stanford.edu/ Protégé] (NO)
+Interactive session (WC/NO/BS)
+Target text for interactive session:
+:Mary Ceusters, a 54 year old non-smoking female, arrives at a Buffalo General Hospital on August 12th, 2007 and Nurse Smith takes her blood pressure and records 160/90mmHg. Based on this reading, Nurse Smith concludes Mary has high blood pressure and prescribes the drug Bumetanide. On July 11, 2009, Mary Ceusters arrives at Erie County Medical Center complaining of sudden chest pains and Doctor Searle conducts an external examination and concludes Mary has suffered a heart-attack, which he suspects is likely the result of coronary artery disease exacerbated by hypertension.
+== 10/17/2016 Ontology, Logic and Software (WC/AR)==
+[https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0098-5 Diagnosis, misdiagnosis, lucky guess, hearsay, and more] (WC)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part1.pptx Slides]
+Language vs. Ontology ([https://scholar.google.com/citations?user=tIcr1AkAAAAJ&hl=en AR])
+What is a ((Health)Care) Process? We have the words. But they are used casually and ambiguously. How do we sort this out? (AR)
+The Web Ontology Language (OWL): What it is and how to relate it to Ontology. A quick introduction to OWL including problems when OWL is used to build ontologies (AR)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part2.pdf Slides]
-Course Description:  This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experimentation and patient care, and show how ontologies are used in accessing, maintaining and exploiting these data and information. It will show how biomedical ontologies are developed and provide a comparative critical analysis of major current biomedical ontologies as well as the methods and tools for biomedical ontology development and evaluation.
+== 10/24/2016 Representing Types and Representing Instances (WC) ==
-Course Outline:   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.
-== '''Recommended background reading''' ==
+Introduction to [http://www.referent-tracking.com/RTU/?page=reftrackparadigm.phtml Referent Tracking] (WC)
-:R. Arp, B. Smith, A. D. Spear, ''[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]''
+Application of Referent Tracking to deal with Errors in Databases (WC)
-== 9/5/2016  Labor Day (no class) ==
-== 9/12/2016  Introduction to Ontology ==
-== 9/19/2016  Ontology of Experiments ==
-The generation & dissemination of new knowledge via biomedical/clinical research & its publication
-== 9/26/2016  Ontology of Clinical Practice ==
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-8.pptx Slides]
-Electronic Health Records and other systems and techniques for modeling, representing & maintaining patient data
-== 10/3/2016  The Gene Ontology and the Open Biomedical Ontologies Foundry ==
+== 10/31/2016 Overview of Ontology: BFO, GO, OBO Foundry (BS) ==
 History and current theoretical foundations for the development of effective biomedical ontologies
-== 10/10/2016  Review of the logical principles for building consistent, structured ontological representations of biomedical data, information & knowledge, capable of interpretation by both humans and computers==
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-9.pptx Slides]
-== 10/17/2016  Building consistent, structured ontological representations of biomedical information (cont.)==
-== 10/24/2016  Introduction to the open source Protégé ontology editor and it’s add-on tools(WC) ==
+*[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration]
-== 10/31/2016 Laboratory exercises & problems ==
+*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104413/ Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]
-== 11/7/2016  The Unified Medial Language System (UMLS) and it’s Semantic Network==
-== 11/14/2016  The SNOMED clinical terminology and ontology==
+== 11/7/2016 Ontology and Terminology (WC / AR)==
-== 11/21/2016  Ontology of Social Entities ==
-Representation of race, gender, and other demographic entities; patient consent; healthcare organizations
+The Ontology for Oral Health and Disease ([http://www2.unb.ca/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_63.pdf OHD]) (AR)
+Ontology and Terminology: An Introduction (WC)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-10.pptx Slides]
+*[http://www.openclinical.org/medicalterminologies.html Medical Terminologies]
+== 11/14/2016  Introduction to SNOMED  (WC/NO)==
+SNOMED: Systematized Nomenclature for Medicine (WC)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-11-part1.pptx Slides]
+Using [http://protege.stanford.edu/ Protégé] ([http://www.jneilotte.com/ Neil Otte])
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-11-part2.pptx Slides]
+== 11/21/2016 Internet of Things / Concluding Summary (WC/BS)==
+SNOMED (continued) (WC)
+The Internet of Things (Biomedical Applications (WC) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part1.pptx Slides]
+*[http://www.referent-tracking.com/RTU/sendfile/?file=CeustersBonaParis2016ReadyForPublication.pdf Tracking Data Quality through the Internet of Things] [http://www.referent-tracking.com/RTU/sendfile/?file=STC2016-Slides.pptx Slides]
+Concluding Summary -- What you should have learned from this class (BS)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part2.pptx Slides]
+Coda on SNOMED (WC)
+[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part3.pdf Slides]
 == 11/28/2016  Student presentations ==
+*4:00 James Schuler: '''The Ontology of Diabetes Camp'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Schuler.pptx Slides]
+:[https://www.youtube.com/watch?v=URMWuBZd-4A Video]
+*4:20 Jonathan Blaisure: '''OMOP'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Blaisure.pptx Slides]
+:[https://youtu.be/23K3_FOXVjA Video]
+*4:40 Sarah Mullin: '''The Ontology of Biological and Clinical Statistics'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Mullin.pdf Slides]
+:[https://youtu.be/y9LTbsYlGBY Video]
+*5:00 Francesco Franda: '''Organizations: An Ontological Approach'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Franda.pptx Slides]
+:[https://youtu.be/smyTVlkY_QI Video]
+*5:20 Fernanda Farinelli: '''Ontology of Document Templates'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Farinelli.pptx Slides]
+:[https://www.youtube.com/watch?v=X3FVwSqZhag Video]
+*5:40 Cameron Bosinski: '''The Origin of Information'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Bosinski.pptx Slides]
+:[https://youtu.be/QNYJCip79FI Video]
+*6:00 Uriah Burke: '''The Zika Virus'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Burke.pptx Slides]
+:[https://www.youtube.com/watch?v=C5PDE02nEPw Video]
 == 12/5/2016  Student presentations ==
+*4:00 Qiuyi Zhang: '''Understanding Accessibility in Healthcare Facilities'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/QZhang.pptx Slides]
+:[https://youtu.be/oz0bmykt820 Video]
+*4:20 Scott Luan: '''On the Ontology of (Biomedical) Artifacts'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Luan.pptx Slides]
+*4:40 Matthew Hudson: '''Disease surveillance through the lens of ontology'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Hudson.pptx Slides]
+*5:00 Ruoyu Yang and Binbin Zhang: '''Ontology of Materials'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Ruoyu.pptx Slides]
+:[https://youtu.be/ufAVzxSlHTU Video]
+*5:20 Munira Binti Mohd Ali: '''Additive Manufacturing in Dentistry'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Ali.pptx Slides]
+:[https://www.youtube.com/watch?v=-tq0TKUtMIc Video]
+*5:40 Federico Borsotti: '''Ontologies and Relational Databases'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Borsotti.pptx Slides]
+:[https://www.youtube.com/watch?v=DobwIniiFFY Video]
+*6:00 Evan Murphy: '''Ontology of Mental Illness'''
+:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Murphy.pptx Slides]
+== Grading Policies ==
-All students will be required to take an active part in class discussions throughout the semester and to prepare a paper on some relevant topic. The paper should be submitted in a draft version on or before October 31, and in final form on or before December 5. A powerpoint version will be presented in class in one or other of the two closing sessions.
+All students will be required to take an active part in class discussions throughout the semester and to prepare a paper on some relevant topic. The paper should be submitted in a draft version on or before October 17, and in final form on or before December 5. A powerpoint version will be presented in class in one or other of the two closing sessions.
 Your grade will be determined in three equal portions deriving from:
 :1. class participation (2.5% per class attended)
-:2. paper (3000 words; deadline for draft: March 29; deadline for final version: May 3)
+:2. either a paper (~3000 words) or a combination of ontology and short paper providing documentation of the ontology
 :3. class presentation (graded according to quality of powerpoint slides, quality of delivery, and quality of response to questions)
-For policy regarding incompletes see [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html here]
+For policy regarding incompletes see under "Grading Procedures" [http://grad.buffalo.edu/study/progress/policylibrary.html here]
+=='''Related Policies and Services'''==
+'''Academic integrity''' is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html.
-For academic integrity policy see [http://www.grad.buffalo.edu/policies/academicintegrity.php here]
+'''Accessibility resources:''' If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web [http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html here].
-For accessibility services see [http://www.buffalo.edu/accessibility/servc.php here]
+google-site-verification: [http://googlef974fa4fe9d924dc%20.html]

Biomedical Ontology 2016: Difference between revisions

Latest revision as of 11:30, 27 September 2023

Recommended background reading

Recommended background video content

Schedule

8/29/2016 Introduction to Ontology 1: General Overview (BS)

9/12/2016 Ontology of Clinical Practice (WC)

9/19/2016 Ontology of Experiments (WC, BS)

9/26/2016 Introduction to Ontology 2: Ontology in Buffalo (BS)

10/3/2016 Ontology of Social Entities (BS)

10/10/2016 How to Build an Ontology (BS/WC/NO)

10/17/2016 Ontology, Logic and Software (WC/AR)

10/24/2016 Representing Types and Representing Instances (WC)

10/31/2016 Overview of Ontology: BFO, GO, OBO Foundry (BS)

11/7/2016 Ontology and Terminology (WC / AR)

11/14/2016 Introduction to SNOMED (WC/NO)

11/21/2016 Internet of Things / Concluding Summary (WC/BS)

11/28/2016 Student presentations

12/5/2016 Student presentations

Grading Policies

Related Policies and Services

Navigation menu

Search