Biomedical Ontology 2016

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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

Recommended background reading

R. Arp, B. Smith, A. D. Spear, Building Ontologies with Basic Formal Ontology

Recommended background video content

Selections from: [1]

Schedule

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

Slides

Roots of ontology in

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

Slides

Disease vs. diagnosis; Electronic Health Records and other systems and techniques for modeling, representing and maintaining patient data

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

Part 1: Ontology of Clinical Practice (continued) (WC)

Slides

Representing clinical data

Part 2: Ontology of Scientific Research (BS)

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

Video: Clinical Trial Data Wants to be Free

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

Slides

Includes a presentation by Alex Diehl on the Cell and Protein Ontologies

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

Slides

Ontology of obligations

Speech act theory

Patient consent

Healthcare organizations

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

Principles of ontology building (BS) Slides

Further principles of ontology building (WC) Slides

First look at 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)

Diagnosis, misdiagnosis, lucky guess, hearsay, and more (WC)

Slides

Language vs. Ontology (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)

Slides

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

Introduction to Referent Tracking (WC)

Application of Referent Tracking to deal with Errors in Databases (WC)

Slides

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

History and current theoretical foundations for the development of effective biomedical ontologies

Slides

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

The Ontology for Oral Health and Disease (OHD) (AR)

Ontology and Terminology: An Introduction (WC)

Slides

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

SNOMED: Systematized Nomenclature for Medicine (WC)

Slides

Using Protégé (Neil Otte)

Slides

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

SNOMED (continued) (WC)

The Internet of Things (Biomedical Applications (WC) Slides

Concluding Summary -- What you should have learned from this class (BS) Slides

Coda on SNOMED (WC) Slides

11/28/2016 Student presentations

  • 4:00 James Schuler: The Ontology of Diabetes Camp
Slides
Video
  • 4:20 Jonathan Blaisure: OMOP
Slides
Video
  • 4:40 Sarah Mullin: The Ontology of Biological and Clinical Statistics
Slides
Video
  • 5:00 Francesco Franda: Organizations: An Ontological Approach
Slides
Video
  • 5:20 Fernanda Farinelli: Ontology of Document Templates
Slides
Video
  • 5:40 Cameron Bosinski: The Origin of Information
Slides
Video
  • 6:00 Uriah Burke: The Zika Virus
Slides
Video

12/5/2016 Student presentations

  • 4:00 Qiuyi Zhang: Understanding Accessibility in Healthcare Facilities
Slides
Video
  • 4:20 Scott Luan: On the Ontology of (Biomedical) Artifacts
Slides
  • 4:40 Matthew Hudson: Disease surveillance through the lens of ontology
Slides
  • 5:00 Ruoyu Yang and Binbin Zhang: Ontology of Materials
Slides
Video
  • 5:20 Munira Binti Mohd Ali: Additive Manufacturing in Dentistry
Slides
Video
  • 5:40 Federico Borsotti: Ontologies and Relational Databases
Slides
Video
  • 6:00 Evan Murphy: Ontology of Mental Illness
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 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. 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 under "Grading Procedures" 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.

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 here.

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