Workshop on Clinical Trial Ontology

General Information

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The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Clinical Trials. The workshop will take place on May 16-17, 2007 at the NIH Campus in Bethesda, MD.

The meeting will be divided into two parts. Day 1 will be a public event consisting of presentations and panel discussions on the CTO and cognate initiatives. Day 2 will be a working meeting devoted to intense discussions of mature drafts of the CTO and to the creation of a strategy for its further development and testing.

The work of the NCBO is funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found here.

We are grateful to the National Heart, Lung and Blood Institute for generous support for this meeting.

Aim of the Workshop

The aim of the workshop is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.

The Workshop will bring together representatives of all of the major groups involved in clinical trial informatics, design, execution, analysis and standardization, with the goal of achieving a broad consensus on the requirements which the ontology should address and on the most effective means of realizing these requirements.

Goals of the Clinical Trial Ontology Initiative

The proposed CTO should:

(1) fully and faithfully capture the types of entities and relationships involved in clinical trials of any experimental design

(2) comprehend terms like: cohort, randomization, placebo, response, efficacy, control, protocol, null hypothesis, confidence interval, finding, biomarker, primary outcome, secondary outcome, intervention group, experimental design, etc., including also major relevant statistical terms and terms drawn from resources such as the CDISC glossary and all terms needed for the task of meta-analysis of clinical trials;

(3) organize these terms in a structured way, providing definitions and logical relations designed to enhance retrieval of, reasoning with, and integration of the data annotated in its terms.

(4) support trial bank interoperation

(5) form an integral part of the more comprehensive framework of the Ontology for Biomedical Investigations OBI, which itself forms part of the OBO Foundry

(6) draw on and seek maximal alignment with existing clinical trial ontologies, including:

-- the Epoch ontology used by the Immune Tolerance Network

-- the RCT Schema ontology used by theTrial Bank Initiative

(7) rest on a clear understanding of the relation between CTO and an epidemiology study ontology

(8) rest on a clear understanding of the relation between CTO and data-model-oriented initiatives such as CDISC and BRIDG.

(9) meet the requirements of the OBO Foundry, and in particular support an adequate treatment of the distinction between types (surgical intervention, tumor, human being) and instances (Jane's oophorectomy, John's tumor, Fritz)

Agenda

PLEASE ALLOW AN EXTRA 30 MINUTES TO COMPLETE THE NIH SECURITY PROCESS

May 16 Natcher Balcony A

8:00am Continental Breakfast & Registration

9:00am Carol Bean: Introduction

9:10am Susan Shurin, Deputy Director of the National Heart Lung and Blood Institute: Welcome

9:20am Werner Ceusters: How to Build an Ontology

10:00am Discussion

10:15am Refreshment Break

10:30am Chris Mungall: The OBO Foundry

11:00am Jennifer Fostel: The Ontology for Biomedical Investigations

11:30am Richard Scheuermann: Introducing the Clinical Trial Ontology

12:00pm Discussion

12:30pm Lunch Break

1:30pm Ida Sim: The RCT Schema

2:00pm Amar Das: Epoch: An Ontological Framework for Clinical Trial Management

2:30pm Barry Smith: The Clinical Trial Ontology: Creating Consensus

3:30pm Refreshment Break

4:00pm Discussion Session

5:00pm Close

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PLEASE ALLOW AN EXTRA 30 MINUTES TO COMPLETE THE NIH SECURITY PROCESS

May 17 Building 31 Conference Room 10

8:00am Continental Breakfast & Registration

9:00am Session 1: Building the Clinical Trial Ontology

(Moderator: Richard Scheuermann)

10:30am Refreshment Break

11:00am Session 2: Applying the Clinical Trial Ontology

(Moderator: Alan Ruttenberg)

12:30pm Lunch Break

1:30pm Session 3: The Future of the Clinical Trial Ontology

(Moderator: Richard Scheuermann)

3:00pm Refreshments/Close

Participants

Robert Arp -- NCBO, Buffalo, NY

Pat Avery -- Digital Infusion, Inc.

Elaine Ayres -- NIH / Clinical Center

William Barrick -- NIH/NIAID

Carol Bean -- NIH/NHLBI

Maureen Beanan -- NIH/National Center for Research Resources

Elmer Bernstam -- University of Texas Health Science Center at Houston

Olivier Bodenreider -- NIH/NLM

Olga Brazhnik -- NIH/National Center for Research Resources

Constantino Castillo -- The KEVRIC Company, Inc.

Werner Ceusters -- Ontology Research Group, University at Buffalo

Huey Cheung -- NIH/CIT

Ling Chin -- NIH / National Institute on Deafness and Other Communication Disorders

Chris Chute -- NCBO, Mayo Clinic, Rochester, MN

Christian Cocos -- IFOMIS, Saarbrücken, Germany

Elaine Collier -- NIH/National Center for Research Resources

Leo Cousineau -- Information Management Consultants, Reston, VA

Lindsay Cowell -- Duke University

Amar Das -- Stanford Medical Informatics

Kaushal Desai -- AstraZeneca

Stephen Dobson -- Pfizer Global Research and Development

Liju Fan -- Ontology Workshop, LLC

Kerstin Forsberg -- AstraZeneca

Jennifer Fostel -- NIH/NIEHS

Douglas Fridsma -- University of Pittsburgh

Charles P. Friedman -- NIH/CRIIT/NHLBI

Louis J. Goldberg -- University at Buffalo

Peter Good -- NIH/National Human Genome Research Institute

Norbert Graf -- Clinic for Paediatric Oncology and Haematology, Saarland University, Homburg, Germany

Lakshmi M. Grama -- NIH/NCI

Ted Grasela -- Cognigen Corporation, Amherst, NY

Patricia Haggerty -- National Heart, Lung and Blood Institute NHLBI / NIH

Herb Hagler -- University of Texas Southwestern Medical Center

Andrea Harabin -- National Heart, Lung and Blood Institute NHLBI / NIH

William Harlan -- Consultant, National Library of Medicine / NIH

Steve Harris -- Computing Laboratory, University of Oxford

Calvin A. Johnson -- Center for Information Technology CIT / NIH

Warren A. Kibbe -- Northwestern University

William Lau -- Center for Information Technology CIT / NIH

Jamie Lee -- University of Texas Southwestern Medical Center

Yuan Liu -- National Institute of Neurological Diseases and Stroke (NINDS) / NIH

Dan Lyman -- Information Management Consultants, Reston, VA

Charles Mead -- NIH/NCI Center for Biomedical Informatics and Information Technology

Ivan Montoya -- National Institute on Drug Abuse (NIDA) / NIH

Chris Mungall -- Howard Hughes Institute, Berkeley, CA

Robert A. Musson -- NIH / NHLBI

Fabian Neuhaus -– National Institute of Standards and Technology (NIST)

Eric Neumann -- Teranode, Seattle, WA

Jeng-Jong Pan -- National Institute on Drug Abuse (NIDA) / NIH

Dave Parrish -- Immune Tolerance Network, Pittsburgh, PA

Ricardo Pietrobon -- Duke University Medical Center

George O. Redmond -- National Cancer Institute (NCI) / NIH

Alexander Rosenthal -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH

Alan Ruttenberg -- Science Commons (c/o MIT CSAIL)

Laurie M. Ryan -- National Institute on Aging (NIA) / NIH

Jody Sachs -- NIH/National Center for Research Resources

Michael Sayre -- NIH/National Center for Research Resources

Richard Scheuermann -- University of Texas Southwestern Medical Center

Susan Shurin -- National Heart, Lung and Blood Institute NIH / NHLBI

Hua-Chuan Sim -- National Library of Medicine NIH / NLM

Ida Sim -- Trial Bank, University of California at San Francisco Medical Center

Barry Smith -- NCBO, University at Buffalo, NY

Ranjana Srivastava -- Information Management Consultants, Reston, VA

Samson Tu -- Stanford University

Suresh Varghese -- Digital Infuzion, Inc.

Chunhua Weng -- University of Pittsburgh

Trish Whetzel -- University of Pennsylvania

Rebecca Williams -- National Library of Medicine / NIH

Sandhya Xirasagar -- Information Management Consultants, Reston, VA

Alison Yao -- National Institute of Allergy and Infectious Diseases, NIH / NIAID

Venue

Day 1: Balcony A, Building 45 (Natcher), NIH Campus, Bethesda, MD

Day 2: Conference Room 10, Building 31, NIH Campus, Bethesda, MD

Travel to NIH Campus

Links

NCBO Bioportal

Open Biomedical Ontologies

OBO Foundry

Ontology for Biomedical Investigations

Trial Bank

Epoch Ontology

The ACGT Project: Advancing Clinico-Genomic Trials on Cancer

Clinical Trial Ontology Wiki

HCLS Ontology Task Force

A video introduction to ontologies by Barry Smith is available here:

• Realmedia: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm

• Mediaplayer: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV

The second half of this presentation pertains to the building of the Clinical Trial Ontology.

Preliminary Fragment of CTO (for illustration purposes only)

Current OWL version