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

Slides Video

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)

Slides Video

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 Childrens Healthcare of Atlanta.

The ONSTR Workshop is funded by the Childrens 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)