Building
Ontologies for Clinical and Translational Research
Tutorial
and Workshop
Department
of Human Genetics, Emory University, Atlanta, Georgia
Wednesday,
June 29, 2011
Motivation
Increasingly, clinicians are critically dependent on information of
multiple different types to support effective care and clinical research. The fact that this
information comes from a wide variety of heterogeneous sources means that
computers are hindered in exploiting it effectively. Problems arise not least
in translational medicine, where results of biological research need to be
translated into a language which allows them to be used effectively in the
clinical context. One strategy to address this problem involves the use of standard controlled vocabularies, also called ‘ontologies’, to create data resources that are more easily
capable of integration.
The purpose of this tutorial is to provide a basic introduction to
ontology development and use; to illustrate best practices; and to provide a
hands-on illustration of ontology development and evaluation in the domain of
translational research and newborn screening.
Part 1: How to Build Useful Ontologies for Clinical and Translational Research (Barry Smith)
8:30am Breakfast
/ Registration
9:00am Ontology
and Its Applications
·
Success Stories
·
The Gene
Ontology (GO)
·
SNOMED, ICD and
other controlled vocabularies
·
Ontology Design
Principles
·
Ontology
Applications
10:30am Break
10.45am Building Blocks for Biomedical Ontologies
·
Basic Formal
Ontology (BFO)
·
Ontology for
General Medical Science (OGMS)
·
Ontology for
Biomedical Investigations (OBI)
12.15pm Lunch
Part 2: The Ontology for Newborn
Screening Translational Research (ONSTR): A Case Study
1.00pm Introduction
to New Born Screening Disorders
Rani
Singh, PhD, Emory University
1.45 pm Ontology Framework
Sivaram Arabandi,
MD, MS, Evolvers Group
2.00pm The ONSTR Ontology
Prabhu Shankar, MD, MS, Emory University
2.45pm Break
3:00pm The
ONSTR Ontology
Review
by Barry Smith
4.00pm A Query Tool for a Newborn Screening Ontology
Akshaye Dhawan, PhD, Ursinus University
Raj Sunderraman, PhD,
Georgia State University
4.30pm Wrap
up
5.00pm End
Background
This tutorial is one of a series of dissemination events
sponsored by the National Center for Biomedical Ontology (NCBO). It is being
organized as part of a two-day Ontology for Newborn Screening Translational Research (ONSTR) Workshop
organized under the auspices of the Department of Human Genetics, Division of
Medical Genetics, Emory University and Children’s Healthcare of Atlanta.
The ONSTR Workshop is funded by the Children’s Hospital of Atlanta (CHOA) seed grant
and HRSA grant #U22MC03960-04-00. Its
content is solely the responsibility of the organizers and presenters and does
not necessarily represent the views of CHOA or HRSA.
Venue
and Accommodation
The tutorial will be held at the Emory
Conference Center Hotel, 1615 Clifton Road Northeast, Atlanta, on June 29,
2011. Places are limited and interested persons should write as soon as
possible to express their interest in participating. No prior knowledge of
ontology is presupposed, but a background in clinical medicine or in
informatics is required.
Faculty
Barry Smith is a prominent contributor to both
theoretical and applied research in ontology. His pioneering work led to the
formation of the OBO (Open Biomedical
Ontologies) Foundry, a set of resources designed to support information-driven
research in biology and biomedicine. Smith is one of the principal scientists
of the NCBO, a Scientific Advisor to the Gene
Ontology Consortium, and a Principal Investigator on the Protein Ontology and Infectious Disease
Ontology projects.
Sivaram Arabandi is a member
of the visiting faculty at the National Library of Medicine. Sivaram trained as
a Surgeon at Health University and received his Masters in Computer Science
from Cardiff University. He has over 10 years of experience in clinical
informatics and conducts research in using Semantic Web technologies for
interoperability of healthcare data. He has authored the Sleep Domain Ontology, the Core Data
Elements model for Cardiothoracic Surgery (SemanticDB,
Cleveland Clinic), and collaborates with other researchers on the Ontology for General Medical Science
and Infectious Disease
Ontology projects.
Akshaye Dhawan is Assistant Professor of
Computer Science at Ursinus College. He received his
Ph.D. and M.S. in Computer Science from Georgia State University. His
dissertation is focused on distributed algorithms for scheduling in Wireless
Sensor Networks. He has also been a lead on the NeuronBank
Project, an NIH-funded cross-disciplinary project that
aims to catalog information on neurons and their
interconnections in a manner that allows for searching of this information
across different species.
Prabhu Shankar is a
clinical informatician in the Department of Human Genetics, Emory University.
He has received a master's degree in Health Informatics from the University of
Texas at Houston in addition to having an extensive clinical experience as an
internist. His expertise is in incorporating various controlled vocabularies
into electronic health records. He initiated and is leading an ontology project
on the inherited metabolic disease Phenylketonuria (PKU), which is designed to
aid aggregation of follow-up data. He also participates in the development of
Ontology for General Medical Sciences.
Rani Singh is Associate
Professor of Human Genetics and Pediatrics and
Director of the Genetic Metabolic Nutrition Program at Emory. With over
18 years of research and clinical experience in the field of inborn errors of
metabolism (IEM), her clinical research interest focuses on the efficacy of restrictive
diets and genotype/phenotype relationships. She is PI of the Enhanced Genetic
Services and Newborn Screening Collaborative project,
whose goal is to identify gaps in genetic services.
Rajshekhar Sunderraman
is Professor of Computer Science at Georgia State University in Atlanta,
Georgia. His research interests are in deductive databases, logic programming, modeling of incomplete and inconsistent information,
semi-structured data, semantic Web, and modeling of
biological data. He has published over one hundred research papers in leading
computer science journals and conferences and is the author of a leading
textbook Oracle
10g Programming: A Primer, published by Addison Wesley.
Participants
1. Barry Smith (Univ. of Buffalo)
2. Rani H. Singh (Emory University)
3. Prabhu Shankar (Emory University)
4. Sivaram Arabandi
(Evolvers Group)
5. Snezana S Nikolic (Georgia State University)
6. Akshaye Dhawan (Ursinus College)
7. Sham Navathe
(Georgia Institute of Technology)
8. Raj Sunderraman (Georgia State University)
9. Kunal Malhotra (Georgia Institute of Technology)
10. Monosij Dutta-Roy (Georgia Institute of Technology)
11. Tim Morris (Emory University)
12. Regina Eady
(Emory University)
13. Circe Tsui
(Emory University)
14. Jeff Weaver (Emory University)
15. Justin Rykowski
(Emory University)
16. Kristi Eckerson
(Emory University)
17. Syed Ahmad (Emory University)
18. James Jellison (CDC)
19. Jean-Baptiste Kamgang
(CDC)
20. Sridhar Papagari
Sangareddy (CDC)
21. Miguel Torres-Urquidy
(CDC)
22. Geraldine Wade (Clinical Informatics Consulting)
23. Betsy Shackelford (Emory University)
24. Mijung Kim (Georgia Institute of
Technology)