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| '''PHI 548 (seminar, 3 credits). Registration number: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI®num=24057 24057]''' | | '''PHI 637 (seminar, 3 credits). Registration number: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI®num=]''' |
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| '''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''': 1:00-3:50pm, Mondays, Fall Semester 2023 |
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| '''Time''': 4:00-6:50pm, Mondays, Fall Semester 2016 | | '''Room''': Park 141, UB North Campus |
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| '''Room''': Baldy 200-G, UB North Campus | | '''Instructors''': [http://ontology.buffalo.edu/smith/ Barry Smith] (Philosophy) and Emanuele Martinelli (Philosophy, University of Zurich) |
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| '''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: by appointment via [mailto:phismith@buffalo.edu email]; EM: TBA |
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| '''Office hours''': BS: by appointment via [mailto:phismith@buffalo.edu email]; WC: TBA | |
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| '''Course Description''' | | '''Course Description''' |
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| 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.
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| All slides and videos will be made available at [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology this link] | | All slides and videos will be made available at [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology this link] |
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| =='''Recommended background reading''' == | | =='''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]''
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| == '''Recommended background video content''' == | | == '''Recommended background video content''' == |
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| Selections from: [http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013]
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| == '''Schedule''' == | | == '''Schedule''' == |
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| == 8/29/2016 Introduction to Ontology 1: General Overview (BS) == | | == August 26: Introduction / General Overview (BS) == |
| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-1.pptx Slides]
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| Roots of ontology in
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| *artificial intelligence ([https://www.academia.edu/722721/The_second_naive_physics_manifesto Second Naive Physics Manifesto])
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| *library science ([https://www.nlm.nih.gov/mesh/subhierarchy.html MeSH])
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| *Semantic Web ([https://en.wikipedia.org/wiki/Web_Ontology_Language OWL])
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| *Human Genome Project ([http://geneontology.org Gene Ontology])
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| == 9/12/2016 Ontology of Clinical Practice (WC) ==
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-2.pptx Slides]
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| Disease vs. diagnosis; Electronic Health Records and other systems and techniques for modeling, representing and maintaining patient data
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| *[http://www.slideserve.com/joben/toward-an-ontology-for-general-medical-science Ontology for General Medical Science]
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| *[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Toward an Ontological Treatment of Disease and Diagnosis]
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| == 9/19/2016 Ontology of Experiments (WC, BS) ==
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| '''Part 1: Ontology of Clinical Practice (continued)''' (WC)
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-3-part1.pptx Slides]
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| Representing clinical data
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| '''Part 2: Ontology of Scientific Research''' (BS)
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-3-part2.pptx Slides]
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| Background on philosophy of science
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| The generation and dissemination of new knowledge through scientific experiments
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| Biomedical research and clinical trials
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| The Information Artifact Ontology
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| *[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154556 Ontology for Biomedical Investigations (OBI)]
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| *[http://ceur-ws.org/Vol-1515/regular10.pdf Information Artifact Ontology]
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| *[http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2015;volume=6;issue=1;spage=37;epage=37;aulast=Smith Image Ontologies]
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| Video: [https://www.youtube.com/watch?v=booqxkpvJMg Clinical Trial Data Wants to be Free]
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| == 9/26/2016 Introduction to Ontology 2: Ontology in Buffalo (BS) ==
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-4.pdf Slides]
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| Includes a presentation by [https://scholar.google.com/citations?user=BUcx6agAAAAJ&hl=en Alex Diehl] on the Cell and Protein Ontologies
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| *[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]
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| *[http://obofoundry.org/ Open Biomedical Ontologies (OBO) Foundry]
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| *[http://obofoundry.org/ontology/iao.html Information Artifact Ontology]
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| *[http://www.referent-tracking.com/RTU/?page=index Referent Tracking]
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| *[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-6 Logical development of the Cell Ontology]
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| *[http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0088-7 The Cell Ontology 2016]
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| *[http://nar.oxfordjournals.org/content/42/D1/D415.long Protein Ontology: a controlled structured network of protein entities]
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| == 10/3/2016 Ontology of Social Entities (BS) ==
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-5.pdf Slides]
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| Ontology of obligations
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| Speech act theory
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| Patient consent
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| Healthcare organizations
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| *[http://ontology.buffalo.edu/document_ontology/ Document Acts]
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| *[http://www.ontobee.org/ontology/d-acts d-acts Ontology]
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| == 10/10/2016 How to Build an Ontology (BS/WC/[http://www.jneilotte.com/ NO])==
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| Principles of ontology building (BS) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-6-part1.pptx Slides]
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| Further principles of ontology building (WC) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-6-part2.pptx Slides]
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| First look at [http://protege.stanford.edu/ Protégé] (NO)
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| Interactive session (WC/NO/BS)
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| Target text for interactive session:
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| :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.
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| == 10/17/2016 Ontology, Logic and Software (WC/AR)==
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| [https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0098-5 Diagnosis, misdiagnosis, lucky guess, hearsay, and more] (WC)
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part1.pptx Slides]
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| Language vs. Ontology ([https://scholar.google.com/citations?user=tIcr1AkAAAAJ&hl=en AR])
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| What is a ((Health)Care) Process? We have the words. But they are used casually and ambiguously. How do we sort this out? (AR)
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| 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)
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part2.pdf Slides]
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| == 10/24/2016 Representing Types and Representing Instances (WC) ==
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| Introduction to [http://www.referent-tracking.com/RTU/?page=reftrackparadigm.phtml Referent Tracking] (WC)
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| Application of Referent Tracking to deal with Errors in Databases (WC)
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-8.pptx Slides]
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| == 10/31/2016 Overview of Ontology: BFO, GO, OBO Foundry (BS) ==
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| History and current theoretical foundations for the development of effective biomedical ontologies
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-9.pptx Slides]
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| *[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration]
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| *[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104413/ Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]
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| == 11/7/2016 Ontology and Terminology (WC / AR)==
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| The Ontology for Oral Health and Disease ([http://www2.unb.ca/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_63.pdf OHD]) (AR)
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| Ontology and Terminology: An Introduction (WC)
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-10.pptx Slides]
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| *[http://www.openclinical.org/medicalterminologies.html Medical Terminologies]
| | == September 2: LABOR DAY (No class) |
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| == 11/14/2016 Introduction to SNOMED (WC/NO)== | | == September 9 == |
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| SNOMED: Systematized Nomenclature for Medicine (WC)
| | == September 16 == |
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-11-part1.pptx Slides]
| | == September 23 == |
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| Using [http://protege.stanford.edu/ Protégé] ([http://www.jneilotte.com/ Neil Otte])
| | == October 7 FALL BREAK (No class) == |
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| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-11-part2.pptx Slides]
| | == October 14 == |
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| == 11/21/2016 Internet of Things / Concluding Summary (WC/BS)== | | == October 21 == |
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| SNOMED (continued) (WC)
| | == October 28 == |
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| The Internet of Things (Biomedical Applications (WC) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part1.pptx Slides]
| | == November 4 == |
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| *[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]
| | == November 11 == |
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| Concluding Summary -- What you should have learned from this class (BS)
| | == November 18 == |
| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part2.pptx Slides]
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| Coda on SNOMED (WC)
| | == November 25 == |
| [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part3.pdf Slides]
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| == 11/28/2016 Student presentations == | | == December 2 == |
| *4:00 James Schuler: '''The Ontology of Diabetes Camp'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Schuler.pptx Slides]
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| :[https://www.youtube.com/watch?v=URMWuBZd-4A Video]
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| *4:20 Jonathan Blaisure: '''OMOP'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Blaisure.pptx Slides]
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| :[https://youtu.be/23K3_FOXVjA Video]
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| *4:40 Sarah Mullin: '''The Ontology of Biological and Clinical Statistics'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Mullin.pdf Slides]
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| :[https://youtu.be/y9LTbsYlGBY Video]
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| *5:00 Francesco Franda: '''Organizations: An Ontological Approach'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Franda.pptx Slides]
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| :[https://youtu.be/smyTVlkY_QI Video]
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| *5:20 Fernanda Farinelli: '''Ontology of Document Templates'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Farinelli.pptx Slides]
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| :[https://www.youtube.com/watch?v=X3FVwSqZhag Video]
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| *5:40 Cameron Bosinski: '''The Origin of Information'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Bosinski.pptx Slides]
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| :[https://youtu.be/QNYJCip79FI Video]
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| *6:00 Uriah Burke: '''The Zika Virus'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Burke.pptx Slides]
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| :[https://www.youtube.com/watch?v=C5PDE02nEPw Video]
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| == 12/5/2016 Student presentations == | | == December 9 Student Presentations == |
| *4:00 Qiuyi Zhang: '''Understanding Accessibility in Healthcare Facilities'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/QZhang.pptx Slides]
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| :[https://youtu.be/oz0bmykt820 Video]
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| *4:20 Scott Luan: '''On the Ontology of (Biomedical) Artifacts'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Luan.pptx Slides]
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| *4:40 Matthew Hudson: '''Disease surveillance through the lens of ontology'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Hudson.pptx Slides]
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| *5:00 Ruoyu Yang and Binbin Zhang: '''Ontology of Materials'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Ruoyu.pptx Slides]
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| :[https://youtu.be/ufAVzxSlHTU Video]
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| *5:20 Munira Binti Mohd Ali: '''Additive Manufacturing in Dentistry'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Ali.pptx Slides]
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| :[https://www.youtube.com/watch?v=-tq0TKUtMIc Video]
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| *5:40 Federico Borsotti: '''Ontologies and Relational Databases'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Borsotti.pptx Slides]
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| :[https://www.youtube.com/watch?v=DobwIniiFFY Video]
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| *6:00 Evan Murphy: '''Ontology of Mental Illness'''
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| :[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Murphy.pptx Slides]
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