Biomedical Ontology 2016

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]

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

Slides

Roots of ontology in

• artificial intelligence (Second Naive Physics Manifesto)
• library science (MeSH)
• Semantic Web (OWL)
• Human Genome Project (Gene Ontology)

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

• Ontology for General Medical Science
• Toward an Ontological Treatment of Disease and Diagnosis

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

• Ontology for Biomedical Investigations (OBI)
• Information Artifact Ontology
• Image Ontologies

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

• Building Ontologies with Basic Formal Ontology
• Open Biomedical Ontologies (OBO) Foundry
• Information Artifact Ontology
• Referent Tracking
• Logical development of the Cell Ontology
• The Cell Ontology 2016
• Protein Ontology: a controlled structured network of protein entities

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

Slides

Ontology of obligations

Speech act theory

Patient consent

Healthcare organizations

• Document Acts
• d-acts Ontology

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)

Slide

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)

An example: the Ontology for Oral Health and Disease OHD (AR)

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

Introduction to Referent Tracking (WC)

Internet of Things (WC)

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

10/31/2016 The Gene Ontology and the Open Biomedical Ontologies Foundry (BS)

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

11/14/2016 The SNOMED clinical terminology and ontology (WC/NO)

SNOMED (WC)

Protege (NO)

11/28/2016 Student presentations

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

12/5/2016 Student presentations

• 4:00 Qiuyi Zhang: Understanding Accessibility in Healthcare Facilities
• 4:20 Scott Luan: On the Ontology of (Biomedical) Artifacts
• 4:40 Matthew Hudson: Viruses
• 5:00 Ruoyu Yang and Binbin Zhang: Ontology of Materials
• 5:20 Munira Binti Mohd Ali: Additive Manufacturing in Dentistry
• 5:40 Federico Borsotti: Ontologies and Relational Databases
• 6:00 Evan Murphy: Ontology of Mental Illness

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.

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)

3. class presentation (graded according to quality of powerpoint slides, quality of delivery, and quality of response to questions)

For policy regarding incompletes see here

For academic integrity policy see here

For accessibility services see here