Difference between revisions of "Workshop on Clinical Trial Ontology"

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== General Information ==
+
== '''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 in May 16-17, 2007 at a venue to be determined.
+
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.  
  
−
== Aim of the workshop  ==
+
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 aim of the workshop is to foster the creation of a reference ontology (high-quality controlled structured vocabulary) for clinical trial annotation. The ontology should 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 [http://www.cdisc.org/glossary/clinicalterminologyv4.pdf glossary.] The ontology will organize these terms in a structured way, providing definitions and logical relations designed to advance reasoning with the data annotated in its terms.
+
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 [http://nihroadmap.nih.gov/bioinformatics 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. It will address the potential uses of CTO, and methodology for CTO design and development.
 +
 
 +
== '''Goals of the Clinical Trial Ontology Initiative''' ==
  
 
The proposed CTO should:
 
The proposed CTO should:
Line 11: Line 21:
 
(1) fully and faithfully capture the types of entities and relationships involved in clinical trials of any experimental design
 
(1) fully and faithfully capture the types of entities and relationships involved in clinical trials of any experimental design
  
−
(2) comprehend all the terms needed for the task of meta-analysis of clinical trials
+
(2) comprehend terms like: ''cohort, randomization, placebo, response, efficacy, control, protocol, null hypothesis, confidence interval, finding, biomarker, primary outcome, secondary outcome, intervention group, confounder,'' etc., including also major relevant statistical terms and terms drawn from resources such as the CDISC [http://www.cdisc.org/glossary/clinicalterminologyv4.pdf 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 [http://obi.sourceforge.net/ OBI], which itself forms part of the [http://obofoundry.org/ OBO Foundry]
 +
 
 +
(6) draw on and seek maximal alignment with existing clinical trial ontologies, including:
 +
 
 +
-- the [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1227 Epoch ontology] used by the [http://www.immunetolerance.org Immune Tolerance Network]
 +
 
 +
-- the [http://rctbank.ucsf.edu/ontology/outline/index.htm RCT Schema] ontology used by the[http://rctbank.ucsf.edu/ Trial Bank Initiative]
 +
 
 +
(7) rest on a clear understanding of the relation between CTO and related ventures such as 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) be created through an open process, in which all interested parties can be involved.
 +
 
 +
== '''Agenda''' ==
 +
 
 +
'''<big><u>Wednesday, May 16 - Building 45 (Natcher), Balcony A</u></big>'''
 +
 
 +
* 8:00am -- Registration & Continental Breakfast
 +
 
 +
'''Session 1 (Chair: Barry Smith)'''
 +
 
 +
* 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'' [http://ontology.buffalo.edu/07/CTO/ceusters.ppt ppt]
 +
 
 +
* 10:00am -- Discussion
 +
 
 +
* 10:15am -- Refreshment Break
 +
 
 +
'''Session 2 (Chair: Dave Parrish)'''
 +
 
 +
* 10:30am -- Chris Mungall: ''The OBO Foundry'' [http://ontology.buffalo.edu/07/CTO/mungall.ppt ppt]
 +
 
 +
* 11:00am -- Jennifer Fostel: ''The Ontology for Biomedical Investigations'' [http://ontology.buffalo.edu/07/CTO/fostel.ppt ppt]
 +
 
 +
* 11:30am -- Richard Scheuermann: ''Introducing the Clinical Trial Ontology'' [http://ontology.buffalo.edu/07/CTO/scheuermann.ppt  ppt]
 +
 
 +
* 12:00pm -- Discussion
 +
 
 +
* 12:30pm -- Lunch Break
 +
 
 +
'''Session 3 (Chair: Werner Ceusters)'''
 +
 
 +
* 1:30pm -- Ida Sim: ''The RCT Schema'' [http://ontology.buffalo.edu/07/CTO/sim.ppt  ppt]
 +
 
 +
* 2:00pm -- Amar Das: ''Epoch: An Ontological Framework for Clinical Trial Management''
 +
[http://ontology.buffalo.edu/07/CTO/Das.pdf ppt]
 +
 
 +
* 2:30pm -- Barry Smith: ''The Clinical Trial Ontology: Creating Consensus'' [http://ontology.buffalo.edu/07/CTO/smith.ppt  ppt]
 +
 
 +
* 3:30pm -- Refreshment Break
 +
 
 +
* 4:00pm -- Discussion Session
 +
 
 +
* 5:00pm -- Close
 +
 
 +
 
 +
'''<big><u>Thursday, May 17 - Building 31, Conference Room 10</u></big>'''
 +
 
 +
* 8:00am -- Registration & Continental Breakfast
 +
 
 +
'''Session 4 (Moderator: Jennifer Fostel)'''
 +
 
 +
* 9:00am -- Building the Clinical Trial Ontology
 +
 
 +
* 10:30am -- Refreshment Break
 +
 
 +
''' Session 5 (Moderator: Alan Ruttenberg)'''
 +
 
 +
* 11:00am -- Applying the Clinical Trial Ontology
 +
**Norbert Graf: ACGT's Clinical Trial Builder [http://ontology.buffalo.edu/07/CTO/graf.ppt ppt]
 +
 
 +
* 12:30pm -- Lunch Break
 +
 
 +
'''Session 6 (Moderator: Richard Scheuermann)'''
 +
 
 +
* 1:30pm -- The Future of the Clinical Trial Ontology [[Media:CTO_Workshop_Day_2_RS_JL.doc]]
 +
 
 +
* 3:00pm -- Close
 +
 
 +
== '''NIH Security Regulations''' ==
 +
 
 +
All visitor vehicles, including taxicabs, hotel and airport shuttles, delivery trucks and vans will be inspected before being allowed on campus. Visitors will be asked to show a form of government-issued photo identification (driver's license, passport, green card, etc.) and to state the purpose of their visit. Be sure to allow extra time for this vehicle inspection procedure. Employees and visitors should continue to wear their identification prominently at all times while on campus.
 +
 +
Guards will remain at certain buildings to address specific program requirements such as sensitive research and safety concerns. At building entrances where guards are posted:
 +
* Visitors may be required to log in, wear a visitors pass and have an employee escort them through the building.
 +
* Visitors may be required to pass through a metal detector and have bags, backpacks or purses inspected or x-rayed as they enter buildings.
 +
Security staff will be looking for and confiscating any suspicious or potentially dangerous materials. U.S. Code prohibits bringing any dangerous weapons onto Federal property, including anything with a blade longer than 2½ inches. Meeting participants may want to leave extra bags or personal materials at their hotel to minimize the time needed for inspection.
 +
 
 +
All visitors including patients, contractors, vendors and delivery persons must use the following entrances:
 +
 +
<u>Rockville Pike at South Drive</u> (Metro):
 +
* Open 24 hours - Inbound and Outbound traffic
 +
* Open to All Vehicles
 +
* Pedestrian Turnstiles Open for Employees
 +
* Gateway Center at Metro Open for Visitor Registration--this is where visitors check-in with security if they are not driving
 +
 
 +
<u>Old Georgetown Road at Center Drive</u> (This entrance is primarily for commercial vehicles and visitors):
 +
* 6am- 7pm -Inbound and Outbound Traffic
 +
* Open to Employee, Commercial and Visitor Vehicles
 +
* Pedestrian Turnstiles Open for Employees
 +
 +
Please note: Visitor parking is limited at NIH. Visitors are encouraged to use public transportation such as the Metrorail subway system which has a convenient stop (Medical Center) on the NIH campus.
 +
 
 +
Visitors arriving by bus will be dropped off at the NIH/Medical Center Metro stop at Rockville Pike and South Drive. Patients and visitors on official business can then ride the Campus Shuttle to the Clinical Center and other designated shuttle stops on the campus.
 +
 
 +
== '''Participants (Final)''' ==
 +
 
 +
Robert Arp -- NCBO, University at Buffalo
 +
 
 +
Elaine Ayres -- NIH / Clinical Center
 +
 
 +
William Barrick -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH
  
−
(3) support trial bank interoperation
+
Carol Bean -- National Heart, Lung and Blood Institute (NHLBI) / NIH
  
−
(4) form an integral part of a more comprehensive investigation ontology, including also the Ontology for Biomedical Investigations [http://obi.sourceforge.net/ OBI], which forms part of the [http://obofoundry.org/ OBO Foundry], and drawing on the [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1227 Epoch ontology] used by the [http://www.immunetolerance.org/ Immune Tolerance Network].
+
Maureen Beanan -- National Center for Research Resources (NCRR) / NIH
  
−
The purpose of the meeting is to bring together representatives of the major groups involved in clinical trial informatics, design, execution, analysis and standardization in order to approve an initial draft of the CTO and create a strategy for its further development and testing.
+
Elmer Bernstam -- University of Texas Health Science Center at Houston
  
−
Further topics to be addressed include:
+
Olivier Bodenreider -- National Library of Medicine (NLM) / NIH
  
−
i. The relation between CTO and data-model-oriented initiatives (HL7, CDISC, BRIDG, caBIG).
+
Olga Brazhnik -- National Center for Research Resources (NCRR) / NIH
  
−
ii. The relation between CTO and a drug (trial) ontology
+
Constantino Castillo -- The KEVRIC Company, Inc.
  
−
iii. The relation between CTO and an epidemiology study ontology
+
Werner Ceusters -- Ontology Research Group, University at Buffalo
  
−
iv. The proper treatment of ''types'' (surgical intervention, tumor, human being) and ''instances'' (Jane's oophorectomy, John's tumor, Fritz) in ontologies and related artifacts.
+
Huey Cheung -- Center for Information Technology (CIT) / NIH
  
−
v. The relation between CTO, Trialbank, and OBD.
+
Ling Chin -- National Institute on Deafness and Other Communication Disorders (NIDCD) / NIH
  
−
== Agenda ==
+
In Hye Cho -- National Library of Medicine (NLM) / NIH
  
−
== Participation ==
+
Christopher G. Chute -- NCBO, Mayo Clinic
  
−
'''PLEASE NOTE THAT PARTICIPATION IN THIS MEETING IS RESTRICTED.'''
+
Kevin Clany -- Invitrogen Corp.
  
−
If you wish to be considered for participation, please send a brief statement to [mailto:phismith@buffalo.edu Barry Smith].
+
Christian Cocos -- IFOMIS (Saarbrücken, Germany)
  
−
== Participants (Provisional List) ==
+
Elaine Collier -- National Center for Research Resources (NCRR) / NIH
  
−
'''All participants will be required to register. Registration details will be available in due course.'''
+
Leo Cousineau -- Information Management Consultants (Reston, VA)
  
−
Carol Bean -- NIH/NHLBI
+
Lindsay Cowell -- Duke University Medical Center
  
−
Werner Ceusters -- NCBO, University at Buffalo
+
Amar Das -- Stanford Medical Informatics
  
−
Chris Chute -- NCBO, Mayo Clinic, Rochester, MN
+
Kaushal Desai -- AstraZeneca
  
−
Lindsay Cowell -- Duke University
+
Stephen Dobson -- Pfizer Global Research and Development
  
 
Liju Fan -- Ontology Workshop, LLC
 
Liju Fan -- Ontology Workshop, LLC
 +
 +
Gabriele Feolo -- National Heart, Lung and Blood Institute (NHLBI) / NIH
  
 
Kerstin Forsberg -- AstraZeneca
 
Kerstin Forsberg -- AstraZeneca
Line 57: Line 191:
 
Jennifer Fostel -- NIH/NIEHS
 
Jennifer Fostel -- NIH/NIEHS
  
−
Gilberto Fragoso -- NIH/NCI
+
Douglas Fridsma -- University of Pittsburgh
  
−
Douglas Fridsma -- University of Pittsburgh
+
Jane Fun -- Contractor, National Library of Medicine (NLM) / NIH
  
 
Louis J. Goldberg -- University at Buffalo
 
Louis J. Goldberg -- University at Buffalo
  
−
Federico Goodsaid -- (FDA CDER, Office of Clinical Pharmacology)
+
Peter Good -- National Human Genome Research Institute (NHGRI) / NIH
 +
 
 +
Norbert Graf -- Clinic for Paediatric Oncology and Haematology, Saarland University (Homburg, Germany)
 +
 
 +
Lakshmi M. Grama -- National Cancer Institute (NCI) / NIH
 +
 
 +
Ted Grasela -- Cognigen Corporation (Amherst, NY)
 +
 
 +
Herb Hagler -- University of Texas Southwestern Medical Center
  
−
Norbert Graf -- [http://acgt.ercim.org/ ACGT], Homburg, Germany
+
Andrea Harabin -- National Heart, Lung and Blood Institute (NHLBI) / NIH
  
−
Ted Grasela -- Cognigen Corporation, Amherst, NY
+
William Harlan -- Consultant, National Library of Medicine (NLM) / NIH
  
 
Steve Harris -- Computing Laboratory, University of Oxford
 
Steve Harris -- Computing Laboratory, University of Oxford
  
−
Tina Hernandez-Boussard -- PharmGKB, Stanford University
+
Frank Hartel -- NCI Center for Bioinformatics / NIH
 +
 
 +
Calvin A. Johnson -- Center for Information Technology (CIT) / NIH
 +
 
 +
Heather A. Junkins -- CRIIT & NHLBI / NIH
 +
 
 +
Webster Kelsey -- Dept of Biomedical Informatics, University of Pittsburgh
 +
 
 +
Warren A. Kibbe -- Northwestern University
 +
 
 +
Bron W. Kisler -- Clinical Data Interchange Standards Consortium (CDISC)
 +
 
 +
George A. Komatsoulis -- NCI Center for Bioinformatics / NIH
 +
 
 +
Jennie Larkin -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
William Lau -- Center for Information Technology (CIT) / NIH
 +
 
 +
Jamie Lee -- University of Texas Southwestern Medical Center at Dallas
 +
 
 +
Natasha Levenkov -- Rockefeller University
 +
 
 +
Yuan Liu -- National Institute of Neurological Diseases and Stroke (NINDS) / NIH
 +
 
 +
Yun Lu -- KAI Research, Inc.
 +
 
 +
Dan Lyman -- Information Management Consultants (Reston, VA)
 +
 
 +
Peter Lyster -- Center for Bioinformatics and Computational Biology, National Institute of General Medical Sciences (NIGMS) / NIH
 +
 
 +
Peter Maccallum -- CRUK Cambridge Research Institute, University of Cambridge
 +
 
 +
Charles Mead -- NCI/NIH, Center for Biomedical Informatics and Information Technology
 +
 
 +
Chris Mungall -- NCBO, Lawrence Berkeley National Laboratory
 +
 
 +
Robert A. Musson -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
Darren Natale -- Georgetown University Medical Center
 +
 
 +
Fabian Neuhaus -– National Institute of Standards and Technology (NIST)
  
−
Randy Levin -- CDER
+
Eric Neumann -- Teranode (Seattle, WA)
  
−
Suzanna Lewis -- NCBO, Berkeley, CA
+
Eduardo Ortiz -- National Heart, Lung and Blood Institute (NHLBI) / NIH
  
−
Peter Maccallum -- UK CancerGrid, Department of Oncology, University of Cambridge
+
Jeng-Jong Pan -- National Institute on Drug Abuse (NIDA) / NIH
  
−
Chris Mungall -- Howard Hughes Institute, Berkeley, CA
+
Dave Parrish -- Immune Tolerance Network (Pittsburgh, PA)
  
−
Mark Musen -- NCBO, Stanford University, CA
+
George O. Redmond -- National Cancer Institute (NCI) / NIH
  
−
Fabian Neuhaus -– NCBO, University at Buffalo, NY
+
Dianne M. Reeves -- National Cancer Institute, Center for Biomedical Informatics and Information Technology (formerly NCICB) / NIH
  
−
Dave Parrish -- Immune Tolerance Network, Pittsburgh, PA
+
Alan Ruttenberg -- Science Commons (c/o MIT CSAIL)
  
−
Philippe Rocca-Serra -- EBI, Hinxton, Cambridge
+
Jody Sachs -- National Center for Research Resources (NCRR) / NIH
  
−
Nigam Shah -– NCBO, Stanford Medical Informatics
+
Michael Sayre -- National Center for Research Resources (NCRR) / NIH
  
−
Susanna Sansone -- EBI, Hinxton, Cambridge
+
Richard Scheuermann -- University of Texas Southwestern Medical Center
  
−
Ida Sim -- NCBO, University of California at San Francisco Medical Center
+
Susan Shurin -- National Heart, Lung and Blood Institute (NHLBI) / NIH
  
−
Barry Smith -– NCBO, University at Buffalo
+
Hua-Chuan Sim -- National Library of Medicine (NLM) / NIH
  
−
Holger Stenzhorn -- IFOMIS, Saarbrücken
+
Ida Sim -- Trial Bank, University of California at San Francisco Medical Center
  
−
Weida Tong -- Center for Toxicoinformatics, FDA NCTR
+
Barry Smith -- NCBO, University at Buffalo
  
−
Trish Whetzel -- University of Pennsylvania
+
Ranjana Srivastava -- Information Management Consultants (Reston, VA)
  
 
Samson Tu -- Stanford University
 
Samson Tu -- Stanford University
  
−
Gabriele Weiler -- Fraunhofer Institute, Sankt Ingbert, Germany
+
Suresh Varghese -- Digital Infuzion, Inc.
  
 
Chunhua Weng -- University of Pittsburgh
 
Chunhua Weng -- University of Pittsburgh
  
−
== Venue ==
+
Rebecca Williams -- National Library of Medicine (NLM) / NIH
 +
 
 +
Ashley Xia -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH
 +
 
 +
Sandhya Xirasagar -- Information Management Consultants (Reston, VA)
 +
 
 +
Alison Yao -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH
 +
 
 +
Zhensheng Zhang -- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) / NIH
 +
 
 +
== '''Venue''' ==
 +
 
 +
Day 1: Balcony A, Building 45 (Natcher), NIH Campus, Bethesda, MD
 +
 
 +
Day 2: Conference Room 10, Building 31, NIH Campus, Bethesda, MD
 +
 
 +
A printable NIH Visitors Map can be found at: [http://parking.nih.gov/documents/visitorAccessMap.pdf NIH Visitors Map]
 +
 
 +
A printable schedule of shuttle service between area hotels and NIH can be found at:  [http://dtts.ors.od.nih.gov/documents/south_hotel_shuttles.pdf NIH Shuttles]
 +
 
 +
== '''Links''' ==
 +
 
 +
[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]
 +
 
 +
[http://obo.sourceforge.net Open Biomedical Ontologies]
 +
 
 +
[http://obofoundry.org OBO Foundry]
 +
 
 +
[http://obi.sourceforge.net Ontology for Biomedical Investigations]
 +
 
 +
[http://rctbank.ucsf.edu/ Trial Bank]
 +
 
 +
[http://protege.stanford.edu/conference/2006/submissions/slides/3.2_Shankar_EpochModels.pdf Epoch Ontology]
 +
 
 +
[http://www.ifomis.uni-saarland.de/wiki/index.php/ACGT The ACGT Project]: Advancing Clinico-Genomic Trials on Cancer
 +
 
 +
[http://www.bioontology.org/wiki/index.php/CTO:Main_Page Clinical Trial Ontology Wiki]
 +
 
 +
[http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM 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) ==
  
−
== Links and Literature ==
+
[http://cto.googlecode.com/svn/trunk/CTO.owl Current OWL version]
  
−
; A problem oriented medical record OWL ontology
+
[[Image:CTO.jpg]]
−
: [http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Dec/0002.html Thread on w3c semweb HCLS list]
 
−
: [http://esw.w3.org/topic/HCLS/POMROntology Description of ontology]
 

Latest revision as of 10:38, 6 August 2008

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.

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. It will address the potential uses of CTO, and methodology for CTO design and development.

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, confounder, 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 related ventures such as 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) be created through an open process, in which all interested parties can be involved.

Agenda

Wednesday, May 16 - Building 45 (Natcher), Balcony A

  • 8:00am -- Registration & Continental Breakfast

Session 1 (Chair: Barry Smith)

  • 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 ppt
  • 10:00am -- Discussion
  • 10:15am -- Refreshment Break

Session 2 (Chair: Dave Parrish)

  • 10:30am -- Chris Mungall: The OBO Foundry ppt
  • 11:00am -- Jennifer Fostel: The Ontology for Biomedical Investigations ppt
  • 11:30am -- Richard Scheuermann: Introducing the Clinical Trial Ontology ppt
  • 12:00pm -- Discussion
  • 12:30pm -- Lunch Break

Session 3 (Chair: Werner Ceusters)

  • 1:30pm -- Ida Sim: The RCT Schema ppt
  • 2:00pm -- Amar Das: Epoch: An Ontological Framework for Clinical Trial Management

ppt

  • 2:30pm -- Barry Smith: The Clinical Trial Ontology: Creating Consensus ppt
  • 3:30pm -- Refreshment Break
  • 4:00pm -- Discussion Session
  • 5:00pm -- Close


Thursday, May 17 - Building 31, Conference Room 10

  • 8:00am -- Registration & Continental Breakfast

Session 4 (Moderator: Jennifer Fostel)

  • 9:00am -- Building the Clinical Trial Ontology
  • 10:30am -- Refreshment Break

Session 5 (Moderator: Alan Ruttenberg)

  • 11:00am -- Applying the Clinical Trial Ontology
    • Norbert Graf: ACGT's Clinical Trial Builder ppt
  • 12:30pm -- Lunch Break

Session 6 (Moderator: Richard Scheuermann)

  • 3:00pm -- Close

NIH Security Regulations

All visitor vehicles, including taxicabs, hotel and airport shuttles, delivery trucks and vans will be inspected before being allowed on campus. Visitors will be asked to show a form of government-issued photo identification (driver's license, passport, green card, etc.) and to state the purpose of their visit. Be sure to allow extra time for this vehicle inspection procedure. Employees and visitors should continue to wear their identification prominently at all times while on campus.

Guards will remain at certain buildings to address specific program requirements such as sensitive research and safety concerns. At building entrances where guards are posted:

  • Visitors may be required to log in, wear a visitors pass and have an employee escort them through the building.
  • Visitors may be required to pass through a metal detector and have bags, backpacks or purses inspected or x-rayed as they enter buildings.

Security staff will be looking for and confiscating any suspicious or potentially dangerous materials. U.S. Code prohibits bringing any dangerous weapons onto Federal property, including anything with a blade longer than 2½ inches. Meeting participants may want to leave extra bags or personal materials at their hotel to minimize the time needed for inspection.

All visitors including patients, contractors, vendors and delivery persons must use the following entrances:

Rockville Pike at South Drive (Metro):

  • Open 24 hours - Inbound and Outbound traffic
  • Open to All Vehicles
  • Pedestrian Turnstiles Open for Employees
  • Gateway Center at Metro Open for Visitor Registration--this is where visitors check-in with security if they are not driving

Old Georgetown Road at Center Drive (This entrance is primarily for commercial vehicles and visitors):

  • 6am- 7pm -Inbound and Outbound Traffic
  • Open to Employee, Commercial and Visitor Vehicles
  • Pedestrian Turnstiles Open for Employees

Please note: Visitor parking is limited at NIH. Visitors are encouraged to use public transportation such as the Metrorail subway system which has a convenient stop (Medical Center) on the NIH campus.

Visitors arriving by bus will be dropped off at the NIH/Medical Center Metro stop at Rockville Pike and South Drive. Patients and visitors on official business can then ride the Campus Shuttle to the Clinical Center and other designated shuttle stops on the campus.

Participants (Final)

Robert Arp -- NCBO, University at Buffalo

Elaine Ayres -- NIH / Clinical Center

William Barrick -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH

Carol Bean -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Maureen Beanan -- National Center for Research Resources (NCRR) / NIH

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

Olivier Bodenreider -- National Library of Medicine (NLM) / NIH

Olga Brazhnik -- National Center for Research Resources (NCRR) / NIH

Constantino Castillo -- The KEVRIC Company, Inc.

Werner Ceusters -- Ontology Research Group, University at Buffalo

Huey Cheung -- Center for Information Technology (CIT) / NIH

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

In Hye Cho -- National Library of Medicine (NLM) / NIH

Christopher G. Chute -- NCBO, Mayo Clinic

Kevin Clany -- Invitrogen Corp.

Christian Cocos -- IFOMIS (Saarbrücken, Germany)

Elaine Collier -- National Center for Research Resources (NCRR) / NIH

Leo Cousineau -- Information Management Consultants (Reston, VA)

Lindsay Cowell -- Duke University Medical Center

Amar Das -- Stanford Medical Informatics

Kaushal Desai -- AstraZeneca

Stephen Dobson -- Pfizer Global Research and Development

Liju Fan -- Ontology Workshop, LLC

Gabriele Feolo -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Kerstin Forsberg -- AstraZeneca

Jennifer Fostel -- NIH/NIEHS

Douglas Fridsma -- University of Pittsburgh

Jane Fun -- Contractor, National Library of Medicine (NLM) / NIH

Louis J. Goldberg -- University at Buffalo

Peter Good -- National Human Genome Research Institute (NHGRI) / NIH

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

Lakshmi M. Grama -- National Cancer Institute (NCI) / NIH

Ted Grasela -- Cognigen Corporation (Amherst, NY)

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 (NLM) / NIH

Steve Harris -- Computing Laboratory, University of Oxford

Frank Hartel -- NCI Center for Bioinformatics / NIH

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

Heather A. Junkins -- CRIIT & NHLBI / NIH

Webster Kelsey -- Dept of Biomedical Informatics, University of Pittsburgh

Warren A. Kibbe -- Northwestern University

Bron W. Kisler -- Clinical Data Interchange Standards Consortium (CDISC)

George A. Komatsoulis -- NCI Center for Bioinformatics / NIH

Jennie Larkin -- National Heart, Lung and Blood Institute (NHLBI) / NIH

William Lau -- Center for Information Technology (CIT) / NIH

Jamie Lee -- University of Texas Southwestern Medical Center at Dallas

Natasha Levenkov -- Rockefeller University

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

Yun Lu -- KAI Research, Inc.

Dan Lyman -- Information Management Consultants (Reston, VA)

Peter Lyster -- Center for Bioinformatics and Computational Biology, National Institute of General Medical Sciences (NIGMS) / NIH

Peter Maccallum -- CRUK Cambridge Research Institute, University of Cambridge

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

Chris Mungall -- NCBO, Lawrence Berkeley National Laboratory

Robert A. Musson -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Darren Natale -- Georgetown University Medical Center

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

Eric Neumann -- Teranode (Seattle, WA)

Eduardo Ortiz -- National Heart, Lung and Blood Institute (NHLBI) / NIH

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

Dave Parrish -- Immune Tolerance Network (Pittsburgh, PA)

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

Dianne M. Reeves -- National Cancer Institute, Center for Biomedical Informatics and Information Technology (formerly NCICB) / NIH

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

Jody Sachs -- National Center for Research Resources (NCRR) / NIH

Michael Sayre -- National Center for Research Resources (NCRR) / NIH

Richard Scheuermann -- University of Texas Southwestern Medical Center

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

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

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

Barry Smith -- NCBO, University at Buffalo

Ranjana Srivastava -- Information Management Consultants (Reston, VA)

Samson Tu -- Stanford University

Suresh Varghese -- Digital Infuzion, Inc.

Chunhua Weng -- University of Pittsburgh

Rebecca Williams -- National Library of Medicine (NLM) / NIH

Ashley Xia -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH

Sandhya Xirasagar -- Information Management Consultants (Reston, VA)

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

Zhensheng Zhang -- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) / NIH

Venue

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

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

A printable NIH Visitors Map can be found at: NIH Visitors Map

A printable schedule of shuttle service between area hotels and NIH can be found at: NIH Shuttles

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

CTO.jpg

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