Immunology Workshop

Ontology Workshop: Focus on Immunology

Dates – March 21-22, 2006 Place – Bethesda, Maryland

---

Background

An ontology is a formal way of representing knowledge. Ontologies provide a computational framework for assimilating biomedical content, integrating existing data and knowledge resources, and improving knowledge sharing. As biomedical research accelerates into the era in which researchers collect and analyze data from mutliple data and knowledge sources in cyberspace, ontologies are critical for annotating experimental and clinical data, for enabling data integration, and for driving intelligent decision-support systems.

DAIT currently supports numerous large contracts that require extensive database development or use, including the Modeling Immunity for Biodefense Centers; Bioinformatics Integration Support Contract; Immune Epitope Database and Analysis Program; Population Genetics; and Immune Tolerance Network. As the DAIT programs develop, the need for an immune system–focused ontology is becoming apparent. Several formal ontologies currently exist, but they do not contain adequate immunological terms. An immunology-based ontology is critically important in order to catalog data and information logically and in such a way that it is easily retrieved from the databases being generated under many DAIT-sponsored awards. A commonly-used ontology will also promote interoperability among the DAIT programs.

---

Goals

The main goals of this workshop are to: • Foster interactions and collaborations among DAIT awardees for the development of a unified ontology for the immune system • Establish standards and compatibility in different ontology frameworks • Provide a forum for the discussion of new and ongoing research and projects using or developing an immune-based ontology • Exchange ideas, technologies and approaches • Seek community awareness.

---

Agenda

March 21, 2006; DAY 1

8:30-9:00am Sign-in/Refreshments

9:00-9:10am: Welcome and Opening Remarks

• Cheryl Kraft, Associate Director, Office of Biomedical Informatics, Division of Allergy, Immunology, and Transplantation (DAIT), NIAID

9:10-9:20am: Logistics/Meeting Goals

• Alison Deckhut Augustine, Chief, Immunoregulation Section, Basic Immunology Branch, DAIT, NIAID

Session I Overview and Foundation for Biomedical Ontologies (Mark Musen, Chair)

9:20-9:50am: Overview

• Barry Smith, Ph.D, Distinguished Professor of Philosophy and Director of the National Center for Ontological Research, Research Director of the European Centre for Ontological Research

9:50-10:20am: Building and Managing Ontologies

• Mark Musen, MD, PhD, Professor, Head of the Stanford Medical Informatics, Stanford University.

10:20- 10:30am: BREAK

10:30 – 11:00am: Development and Maintenance of the GO Ontology

• Michael Ashburner, PhD, Professor of Biology, University of Cambridge

11:00 – 11:30am: Foundational Model of Anatomy – Ontology Building Block

• Cornelius Rosse, M.D., D.Sc., Professor Emeritus, Departments of Biological Structure, and Medical Education and Biomedical Informatics, School of Medicine, University of Washington

11:30am– 12:00pm UMLS and Semantic Web

• Olivier Bodenreider, PhD, National Center for Biomedical Communications, National Library of Medicine, NIH

12:00- 12:10pm Conclusions from Session I (Mark Musen, Chair)

12:10 – 1:30pm: LUNCH

Session II Domain Knowledge Representation in Ontologies (Frank Hartel, Chair)

1:30 – 2:00pm: NCI Thesaurus

• Frank Hartel, PhD, Director of Enterprise Vocabulary Services, Center for Bioinformatics, National Cancer Institute

2:00- 2:30pm Mammalian Phenotype Ontology

• Judith Blake, PhD, Associate Staff Scientist, The Jackson Laboratory

2:30 - 3:00pm: GALEN - Clinical Ontology

• Alan Rector, MD, PhD, University of Manchester

3:00 - 3:10 pm: BREAK

3:10 – 3:40pm IMGT – Ontology for Immunogenetics and Immunoinformatics

• Marie-Paule Lefranc, PhD, Laboratoire d'ImmunoGenetique Moleculaire, Universite Montpellier II, and Institut Universitaire de France

3:40 – 4:10pm Representation of Immunology in GO

• Alexander Diehl, PhD, Scientific Curator, MGI, The Jackson Labatory

4:10 – 5:00pm General Discussion – Best practices for Ontology Design/Development Methods

• Mark Musen and Frank Hartel - Moderators

5:00pm ADJOURN

March 22, 2006; DAY 2

8:30 – 9:00am Refreshments

Session III Immune Ontology Development by DAIT-supported Investigators

9:00 – 9:30am BISC (Bioinformatics Support Contract)

• Richard Scheuermann, PhD, Professor, Director, Division of Translational Pathology, Departmetn of Pathology, University of Texas Southwest Medical Center

9:30 – 10:00am Innate Immunity Ontology - Duke Immune Modeling Center

• Lindsay Grey Cowell, PhD, Assistant Professor, Department of Biostatistics and Bioinformatics, Duke University Laboratory of Computational Immunology, Center for Bioinformatics and Computational Biology

10:00 – 10:30am Immune Epitope Database (IEDB) Knowledge Representation

• Alessandro Sette, PhD, Head, Division of Translational Immunology, La Jolla Institute for Allergy and Immunology

10:30 – 10:40am BREAK

10:40 – 11:10am Immune Tolerance Network

• Amar Das, MD, PhD, Assistant Professor, Departments of Medicine, Psychiatry, and Behavioral Sciences, Stanford University.

11:10 – 11:40am Inner City Asthma Consortium

• Herman Mitchell, PhD, Rho Federal Systems Division, Inc
• Dennis Wallace, PhD, Rho Federal Systems Division, Inc

11:40 – 1:30pm Group Discussion (working lunch)

• Topics to be addressed and discussed:

• Examine the coverage of ontologies of the immune system:
• Identify existing compatible and complementary Immune Ontologies
• Identify gaps in representing immunological knowledge
• Analysis and understanding of the technical problems related to integration of contexts and ontologies from theoretical, practical and application perspective
• Develop plan for collaborations in Immune Ontology development

1:30pm ADJOURN