Difference between revisions of "Workshop on Clinical Trial Ontology"

Revision as of 04:06, 26 April 2007

General Information

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

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 and theRCT 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 [Draft]

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.

Please note that active participation in Day 2 of the meeting is restricted. If you wish to be considered for participation, please send a brief statement to Barry Smith.

Observers will be welcome in both parts of the meeting providing they give prior notice, details concerning which will be provided in due course.

May 16 Natcher Balcony A

8.00am Continental Breakfast

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 Coffee

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

12.00 noon Discussion

12.30 Lunch

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

3.00pm Discussion

3.30pm Coffee

4.00pm Panel Session

5.00pm Close

May 17 Building 31 Conference Room 10

8.00am Continental Breakfast

9.00am Session 1: Building the Clinical Trial Ontology

Moderator: Richard Scheuermann

10.30am Coffee

11.00am Session 2: Applying the Clinical Trial Ontology

12.30 noon Lunch

1.30pm Session 3: The Future of the Clinical Trial Ontology

3.00pm Coffee

Participants

Sivaram Arabandi -- Cleveland Clinic

Robert Arp -- NCBO, Buffalo, NY

Pat Avery -- Digital Infusion, Inc.

Charles E. Barr -- AMIA Clinical Trial Working Group

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

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

Gilberto Fragoso -- NIH/NCI

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

Federico Goodsaid -- FDA CDER, Office of Clinical Pharmacology

Norbert Graf -- ACGT, 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

Steve Harris -- Computing Laboratory, University of Oxford

Tina Hernandez-Boussard -- PharmGKB, Stanford University

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

Warren A. Kibbe -- Northwestern University

Bron W. Kisler -- CDISC Terminology Program

William Lau -- Center for Information Technology CIT / NIH

Jamie Lee -- University of Texas Southwestern Medical Center

Randy Levin -- CDER

Eric Little -- Center for Ontology and Interdisciplinary Studies, Buffalo

Dan Lyman -- Information Management Consultants, Reston, VA

Peter Maccallum -- UK CancerGrid, Department of Oncology, University of Cambridge

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

Chris Mungall -- Howard Hughes Institute, Berkeley, CA

Mark Musen -- NCBO, Stanford University, CA

Robert A. Musson -- NIH / NHLBI

Fabian Neuhaus -– NCBO, University at Buffalo, NY

Eric Neumann -- Teranode, Seattle, WA

Chimezie Ogbuji -- Cleveland Clinic Foundation, OH

Dave Parrish -- Immune Tolerance Network, Pittsburgh, PA

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

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

Jody Sachs -- NIH/National Center for Research Resources

Michael Sayre -- NIH/National Center for Research Resources

Richard Scheuermann -- University of Texas Southwestern Medical Center

Nigam Shah -– NCBO, Stanford Medical Informatics

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

Weida Tong -- Center for Toxicoinformatics, FDA NCTR

Samson Tu -- Stanford University

Suresh Varghese -- Digital Infuzion, Inc.

Chunhua Weng -- University of Pittsburgh

Trish Whetzel -- University of Pennsylvania

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