NCBO Wiki - User contributions [en]

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-03-19T15:52:42Z

Scheuerm:

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012. Day 1 will provide a survey of current ontology-based research in immunology and infectious disease; Day 2 will be focused on flow cytometry; Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, and a session on the Ontology for General Medical Science.

'''Goals'''

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and other fields.

----

'''Draft Schedule'''

''Day 1: Monday, June 11, 2012: 10:00am-5:00pm''

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

:'''Morning: GO, PRO, CL, IO, IEO'''

:Topics to be discussed will include:
::Immune pathway representations
::Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for Immune Epitope Database (IEDB)

:'''Lunchtime talk: Atul Butte (Stanford): Immune Receptors, Inflammation and Type 2 Diabetes'''

:'''Afternoon: IDO and Its Extensions'''

''Day 2: Tuesday, June 12, 2012: 9:00am-5:00pm''

'''Ontologies and Flow Cytometry Informatics'''

:'''Morning: Flow cytometry typing of normal and malignant cell types

:Alexander Diehl
:::Overview of Hematopoietic Cell Types in the Cell Ontology
:::An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes

:Representative of Euroflow Consortium (to be identified): Overview of Euroflow Typing Panels

:(To be identified): Clinical Flow Cytometry in HIV

:Discussion of the ontological treatment of typing panels.

:'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology'''

:Ryan Brinkman:
:::1. Overview of the representation of flow cytometry assays in OBI
:::2. Overview of Flow Cap Competition & flowMeans

:Richard Scheuermann: Connecting results from automated FCM analysis systems with the Cell Ontology

:Cliburn Chan: Flow cytometry analysis system

:Topics to be discussed will include:
::Methods to automatically link flow cytometry results to cell type identification.

''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''

:''9am-noon: TBD''

:'''12pm-3pm Practical Applications of Ontologies in Clinical Research'''
:Topics to be discussed will include:
::Current work on Neurological Disease Ontology
:Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease
::The HIV Ontology

:'''3pm: Closing Session on the Ontology for General Medical Science'''

:''Close: 6:00pm''

----

'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alex Diehl)
:CL Cell ontology immune branches (e.g. for dendritic cells)
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alex Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alex Diehl)

----

'''Participants will include'''

:Ryan Brinkman (University of British Columbia, June 11-12)
:Atul Butte (Stanford University)
:Cliburn Chan (Duke University, June 11-12)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Peter d'Eustachio (New York University, June 11-12)
:Alex Diehl (University at Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters, (University of California at San Diego)
:Alan Ruttenberg (University at Buffalo)
:Richard Scheuermann (University of Texas Southwestern Medical Center)
:Stanley A. Schwartz (University at Buffalo)
:Barry Smith (University at Buffalo)
:Alex C. Yu (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)

IDO Workshop 2010

2010-11-05T17:27:21Z

Scheuerm:

== Background ==

A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for
Biomedical Ontology ([http://bioontology.org NCBO]).

The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all
infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases,
including diseases of bacterial, viral, and eukaryotic origin.

Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to
serve integration of a broad array of -omics, epidemiological and clinical data.

For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.

== Goals of the Meeting ==

*The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency.

*We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:

::clinical data integration
::text and data mining
::genetic susceptibility to infectious disease
::disease surveillance
::plant infectious disease

*The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.

== Schedule ==

'''Tuesday, December 7'''

*7:00pm Dinner (Dutch treat, venue to be announced)

'''Day 1: Wednesday, December 8'''

*8:30am Registration & Continental Breakfast

*9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Cowell and Smith

*9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)
::Scheuermann - VIPR
::TBD - PRIME and ImmPort
::Stoeckert - EuPathDB

*11:00am Refreshment Break

*11:30am Session 1 (continued)
::Sobral - PATRIC and PathogenPortal
::Topalis - VectorDB

*12:30pm Lunch Break

*2:00pm Session 1 (continued)
::General discussion on the utility of IDO as Controlled Vocabulary

*3:30pm Refreshment Break

*4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes)
::Fuentes - Dengue/vector control
::Schober - DeBugIT

*5:30pm End of Day 1

*6:00pm Dinner (Dutch treat, venue to be announced)

'''Day 2: Thursday, December 9: Data Integration Use Cases'''

*8:30am Continental Breakfast

*9:00am Session 3 (Session chair: Goldfain)
::Masci - CFAR
::Schwartz - UB HIV project

*11:00am Refreshment Break

*11:30am Session 4 (Session chair: Ruttenberg)
::Goldfain - SABG
::Courtot - PCIRN

*12:15pm Lunch Break

*1:45pm Session 5 (Session chair: Cowell)
::He - VIOLIN
::Jaswal - Plant IDO
::Cowell - Next Steps

*4:00pm Close of NCBO/IDO 2010 Workshop

'''Format'''

Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.

== Venue ==

A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:

[http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]
1739 West Nursery Road
Linthicum Heights, MD 21090

To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''.

To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]

* NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.

* The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport.

* To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''.

Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]

== Intending Participants ==

Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)

Sivaram Arabandi (Case Western Reserve University)

Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)

Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)

Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)

Alexander Diehl (Gene Ontology / The Jackson Laboratory)

Saul Lozano-Fuentes (Colorado State University)

Albert Goldfain (University at Buffalo)

Yongqun "Oliver" He (University of Michigan Medical Center)

Pankaj Jaiswal (Plant Ontology / Oregon State University)

Jessica Kissinger (Center for Tropical & Emerging Global Diseases / University of Georgia)

Yu Lin (University of Michigan Medical Center)

Joanne Luciano (Predictive Medicine, Inc.)

Supriya Mahajan (University at Buffalo)

Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)

Anna Maria Masci (Duke University Medical Center)

Bjoern Peters (University of California at San Diego)

Jessica Reynolds (University at Buffalo)

Alan Ruttenberg (Science Commons / University at Buffalo)

Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)

Daniel Schober (Universität Freiburg, Germany)

Stanley D. Schwartz (University at Buffalo)

Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)

Barry Smith (NCBO / University at Buffalo)

Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)

Burke Squires (University of Texas Southwestern Medical Center at Dallas)

Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)

Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)

Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)

Patricia Whetzel (NCBO, Stanford)

Allen Xiang (University of Michigan Medical Center)

Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)

DallasWorkshop

2008-09-02T21:04:42Z

Scheuerm: /* Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''

[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas

[http://ontology.buffalo.edu/smith/ Barry Smith], National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''

[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]

[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

[http://www.leadhorsetech.com/LEAD_HORSE_TECHNOLOGIES/Home.html Lead Horse Technologies, Inc.]

''Date:''

September 3-4, 2008

''Venue:''

Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
*To take advantage of discounted rate at the conference hotel, guest room reservations must be secured '''no later than August 15'''. See Workshop registration form for further details.
*There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The goals of the workshop are:

*to utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*to delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*to develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*to take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*to explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Agenda==

'''Day 1: Wednesday, September 3''' (Room: Irving 2 & 3)

8:30am - Registration and Continental Breakfast

9:00am - Opening remarks / Workshop goals (Richard Scheuermann)

9:15am - Session 1: Signs, symptoms and laboratory findings from a health care perspective (Scheuermann, moderator)

::: Combining clinical exam and laboratory findings in the rheumatology clinic (David Karp)
::: Clinical signs and findings in neonatology (Andrew James)

10:30am - Refreshment Break

10:45am - Session 2: Ontology approaches to describing the clinical phenotype (Smith, moderator)

::: Reasoning with clinical exam and laboratory findings: The case of myocardial infarction (Sivaram Arabandi)

12:00pm - Buffet Lunch (Grand Prairie Room), '''''Provided by the generous support of''''' [http://www.leadhorsetech.com/LEAD_HORSE_TECHNOLOGIES/Home.html '''''Lead Horse Technologies, Inc.''''']

1:00pm - Session 3: Standardization of clinical and laboratory data in the context of clinical and translational research (Ruttenberg, moderator)

::: Data standards from patient care to clinical and translational research: The CTSA perspective (Chris Chute)
::: Representation of clinical and laboratory findings in the CDISC SDTM (Bron Kisler)

3:00pm - Refreshment Break

3:30pm - Session 3 continued

::: The future of SNOMED-CT in the representation of clinical findings (Kent Spackman)
::: Problems with current approaches to clinical data (William Hogan)

5:30pm - Reception (Salons G & H), '''''Provided by the generous support of The Cleveland Clinic Foundation SemanticDB'''''

'''Day 2: Thursday, September 4''' (Room: Irving 2 & 3)

8:30am - Continental Breakfast

9:00am - Session 4: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms (Bodenreider, moderator)

::: Laboratory data and metadata in laboratory information systems (Olivier Bodenreider and Anita Burgun)
::: An ontology-based approach for connecting disease pathogenesis with clinical/laboratory data (Richard Scheuermann)

10:30am - Refreshment Break

10:45am - Session 5: How consistent ontological design and development principles can lead to enhanced representation of signs, symptoms, and clinical and laboratory finding (Smith, moderator)
::: PATO and Phenote: From model organism phenotypes to clinical medicine (Suzanna Lewis)

12:00pm - Lunch Break

1:00pm - Session 6: Strategies to achieve convergence of ontologies, vocabularies and data structures in representing signs, symptoms, and clinical and laboratory findings (Scheuermann, moderator)

2:30pm - Refreshment Break

2:45pm - Session 6 (continued)

4:00pm - Close

==Confirmed Participants==

This is a working meeting and participation is restricted.

*Jonas Silva Almeida (MD Anderson Cancer Center / University of Texas)
*Sivaram Arabandi (Heart & Vascular Institute / Cleveland Clinic)
*John M. Armstrong (Lead Horse Technologies, Inc.)
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)
*Bruce Bray (Dept of Biomedical Informatics, University of Utah)
*Anita Burgun (Université de Rennes)
*Kei-Hoi Cheung (Senselab / Yale Center for Medical Informatics)
*Christopher G. Chute (National Center for Biomedical Ontology / Mayo Clinic)
*Paolo Ciccarese (Mass General Hospital / Harvard Medical School)
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)
*Gianluca Colombo (University of Milano-Bicocca, DISCo)
*Tommie G. Curtis (SAIC, NCICB Contractor)
*Amar K. Das (Center for Biomedical Informatics Research / Stanford University)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)
*William Hogan (University of Pittsburgh Medical Center)
*Zhang-Zhi Hu (PRO / Georgetown University Medical Center)
*Charles Jaffe (Health Level 7, Inc. (HL7))
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)
*David Karp (University of Texas Southwestern Medical Center at Dallas)
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)
*Pradeep Mutalik (Yale Center for Medical Informatics)
*Meredith L. Nahm (Duke Translational Medicine Institute)
*Chimezie Ogbuji (Cleveland Clinic Foundation)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)
*John Quinn (Health Level 7, Inc. (HL7))
*Alan Ruttenberg (Science Commons / Neurocommons)
*Neil Sarkar (Marine Biological Laboratory)
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)
*Kent A. Spackman (International Health Terminology Standards Development Organization)
*Larry Streepy (Cleveland Clinic Foundation)
*Nicole Washington (Lawrence Berkeley National Laboratory)
*Ashley Xia (NIAID / NIH)
*W. Jim Zheng (Biomedical Ontology Research Group / Medical University of South Carolina)

In addition to NCBO and the University of Texas Southwestern Medical Center, the following communities are represented: CTSA, HL7, CDISC, OBO, SNOMED, and the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

[http://org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt What is a Diagnosis?], Werner Ceusters

[http://bmir.stanford.edu/file_asset/index.php/1338/BMIR-2008-1302.pdf Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism], Samson W. Tu, Lakshika Tennakoon, Martin O'Connor, Ravi Shankar, and Amar Das.

[http://ontology.buffalo.edu/medo/Williams_Disease.pdf The Factory Model of Disease], Neil Williams.

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-08-25T14:02:07Z

Scheuerm: /* Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''

[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas

[http://ontology.buffalo.edu/smith/ Barry Smith], National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''

[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]

[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''

September 3-4, 2008

''Venue:''

Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
*To take advantage of discounted rate at the conference hotel, guest room reservations must be secured '''no later than August 15'''. See Workshop registration form for further details.
*There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Agenda==

'''Day 1: Wednesday, September 3''' (Room: Irving 2 & 3)

8:30am - Registration and Continental Breakfast

9:00am - Opening remarks / Workshop goals (Richard Scheuermann)

9:15am - Session 1: Signs, symptoms and laboratory findings from a health care perspective (Scheuermann, moderator)

::: Combining clinical exam and laboratory findings in the rheumatology clinic (David Karp)
::: Clinical signs and findings in neonatology (Andrew James)

10:30am - Refreshment Break

10:45am - Session 2: Ontology approaches to describing the clinical phenotype (Smith, moderator)

::: Reasoning with clinical exam and laboratory findings: The case of myocardial infarction (Sivaram Arabandi)

12:00pm - Buffet Lunch (Grand Prairie Room), '''Sponsored by:''' [http://www.leadhorsetech.com/LEAD_HORSE_TECHNOLOGIES/Home.html '''Lead Horse Technologies, Inc.''']

1:00pm - Session 3: Standardization of clinical and laboratory data in the context of clinical and translational research (Ruttenberg, moderator)

::: Data standards from patient care to clinical and translational research: The CTSA perspective (Chris Chute)
::: Representation of clinical and laboratory findings in the CDISC SDTM (Bron Kisler)

3:00pm - Refreshment Break

3:30pm - Session 3 continued

::: The future of SNOMED-CT in the representation of clinical findings (Kent Spackman)
::: Problems with current approaches to clinical data (William Hogan)

5:30pm - Reception (Salons G & H)

'''Day 2: Thursday, September 4''' (Room: Irving 2 & 3)

8:30am - Continental Breakfast

9:00am - Session 4: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms (Bodenreider, moderator)

::: Laboratory data and metadata in laboratory information systems (Olivier Bodenreider and Anita Burgun)
::: An ontology-based approach for connecting disease pathogenesis with clinical/laboratory data (Richard Scheuermann)

10:30am - Refreshment Break

10:45am - Session 5: How consistent ontological design and development principles can lead to enhanced representation of signs, symptoms, and clinical and laboratory finding (Lewis, moderator)
::: PATO and Phenote: From model organism phenotypes to clinical medicine (Suzanna Lewis)

12:00pm - Lunch Break

1:00pm - Session 6: Strategies to achieve convergence of ontologies, vocabularies and data structures in representing signs, symptoms, and clinical and laboratory findings (Scheuermann, moderator)

2:30pm - Refreshment Break

2:45pm - Session 6 (continued)

4:00pm - Close

==Confirmed Participants==

This is a working meeting and participation is restricted.

*Jonas Silva Almeida (MD Anderson Cancer Center / University of Texas)
*Sivaram Arabandi (Heart & Vascular Institute / Cleveland Clinic)
*John M. Armstrong (Lead Horse Technologies, Inc.)
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)
*Bruce Bray (Dept of Biomedical Informatics, University of Utah)
*Anita Burgun (Université de Rennes)
*Kei-Hoi Cheung (Senselab / Yale Center for Medical Informatics)
*Christopher G. Chute (National Center for Biomedical Ontology / Mayo Clinic)
*Paolo Ciccarese (Mass General Hospital / Harvard Medical School)
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)
*Gianluca Colombo (University of Milano-Bicocca, DISCo)
*Tommie G. Curtis (SAIC, NCICB Contractor)
*Amar K. Das (Center for Biomedical Informatics Research / Stanford University)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)
*William Hogan (University of Pittsburgh Medical Center)
*Zhang-Zhi Hu (PRO / Georgetown University Medical Center)
*Charles Jaffe (Health Level 7, Inc. (HL7))
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)
*David Karp (University of Texas Southwestern Medical Center at Dallas)
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)
*Pradeep Mutalik (Yale Center for Medical Informatics)
*Meredith L. Nahm (Duke Translational Medicine Institute)
*Chimezie Ogbuji (Cleveland Clinic Foundation)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)
*John Quinn (Health Level 7, Inc. (HL7))
*Alan Ruttenberg (Science Commons / Neurocommons)
*Neil Sarkar (Marine Biological Laboratory)
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)
*Kent A. Spackman (International Health Terminology Standards Development Organization)
*Larry Streepy (Cleveland Clinic Foundation)
*Nicole Washington (Lawrence Berkeley National Laboratory)
*Ashley Xia (NIAID / NIH)
*W. Jim Zheng (Biomedical Ontology Research Group / Medical University of South Carolina)

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

[http://bmir.stanford.edu/file_asset/index.php/1338/BMIR-2008-1302.pdf Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism], Samson W. Tu, Lakshika Tennakoon, Martin O'Connor, Ravi Shankar, and Amar Das.

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-08-25T13:59:26Z

Scheuerm: /* Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''

[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas

[http://ontology.buffalo.edu/smith/ Barry Smith], National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''

[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]

[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''

September 3-4, 2008

''Venue:''

Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
*To take advantage of discounted rate at the conference hotel, guest room reservations must be secured '''no later than August 15'''. See Workshop registration form for further details.
*There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Agenda==

'''Day 1: Wednesday, September 3''' (Room: Irving 2 & 3)

8:30am - Registration and Continental Breakfast

9:00am - Opening remarks / Workshop goals (Richard Scheuermann)

9:15am - Session 1: Signs, symptoms and laboratory findings from a health care perspective (Scheuermann, moderator)

::: Combining clinical exam and laboratory findings in the rheumatology clinic (David Karp)
::: Clinical signs and findings in neonatology (Andrew James)

10:30am - Refreshment Break

10:45am - Session 2: Ontology approaches to describing the clinical phenotype (Smith, moderator)

::: PATO and Phenote: From model organism phenotypes to clinical medicine (Suzanna Lewis)
::: Reasoning with clinical exam and laboratory findings: The case of myocardial infarction (Sivaram Arabandi)

12:00pm - Buffet Lunch (Grand Prairie Room), '''Sponsored by:''' [http://www.leadhorsetech.com/LEAD_HORSE_TECHNOLOGIES/Home.html '''Lead Horse Technologies, Inc.''']

1:00pm - Session 3: Standardization of clinical and laboratory data in the context of clinical and translational research (Ruttenberg, moderator)

::: Data standards from patient care to clinical and translational research: The CTSA perspective (Chris Chute)
::: Representation of clinical and laboratory findings in the CDISC SDTM (Bron Kisler)

3:00pm - Refreshment Break

3:30pm - Session 3 continued

::: The future of SNOMED-CT in the representation of clinical findings (Kent Spackman)
::: Problems with current approaches to clinical data (William Hogan)

5:30pm - Reception (Salons G & H)

'''Day 2: Thursday, September 4''' (Room: Irving 2 & 3)

8:30am - Continental Breakfast

9:00am - Session 4: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms (Bodenreider, moderator)

::: Laboratory data and metadata in laboratory information systems (Olivier Bodenreider and Anita Burgun)
::: An ontology-based approach for connecting disease pathogenesis with clinical/laboratory data (Richard Scheuermann)

10:30am - Refreshment Break

10:45am - Session 5: How consistent ontological design and development principles can lead to enhanced representation of signs, symptoms, and clinical and laboratory finding (Lewis, moderator)

12:00pm - Lunch Break

1:00pm - Session 6: Strategies to achieve convergence of ontologies, vocabularies and data structures in representing signs, symptoms, and clinical and laboratory findings (Scheuermann, moderator)

2:30pm - Refreshment Break

2:45pm - Session 6 (continued)

4:00pm - Close

==Confirmed Participants==

This is a working meeting and participation is restricted.

*Jonas Silva Almeida (MD Anderson Cancer Center / University of Texas)
*Sivaram Arabandi (Heart & Vascular Institute / Cleveland Clinic)
*John M. Armstrong (Lead Horse Technologies, Inc.)
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)
*Bruce Bray (Dept of Biomedical Informatics, University of Utah)
*Anita Burgun (Université de Rennes)
*Kei-Hoi Cheung (Senselab / Yale Center for Medical Informatics)
*Christopher G. Chute (National Center for Biomedical Ontology / Mayo Clinic)
*Paolo Ciccarese (Mass General Hospital / Harvard Medical School)
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)
*Gianluca Colombo (University of Milano-Bicocca, DISCo)
*Tommie G. Curtis (SAIC, NCICB Contractor)
*Amar K. Das (Center for Biomedical Informatics Research / Stanford University)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)
*William Hogan (University of Pittsburgh Medical Center)
*Zhang-Zhi Hu (PRO / Georgetown University Medical Center)
*Charles Jaffe (Health Level 7, Inc. (HL7))
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)
*David Karp (University of Texas Southwestern Medical Center at Dallas)
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)
*Pradeep Mutalik (Yale Center for Medical Informatics)
*Meredith L. Nahm (Duke Translational Medicine Institute)
*Chimezie Ogbuji (Cleveland Clinic Foundation)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)
*John Quinn (Health Level 7, Inc. (HL7))
*Alan Ruttenberg (Science Commons / Neurocommons)
*Neil Sarkar (Marine Biological Laboratory)
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)
*Kent A. Spackman (International Health Terminology Standards Development Organization)
*Larry Streepy (Cleveland Clinic Foundation)
*Nicole Washington (Lawrence Berkeley National Laboratory)
*Ashley Xia (NIAID / NIH)
*W. Jim Zheng (Biomedical Ontology Research Group / Medical University of South Carolina)

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

[http://bmir.stanford.edu/file_asset/index.php/1338/BMIR-2008-1302.pdf Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism], Samson W. Tu, Lakshika Tennakoon, Martin O'Connor, Ravi Shankar, and Amar Das.

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-08-25T13:57:52Z

Scheuerm: /* Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''

[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas

[http://ontology.buffalo.edu/smith/ Barry Smith], National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''

[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]

[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''

September 3-4, 2008

''Venue:''

Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
*To take advantage of discounted rate at the conference hotel, guest room reservations must be secured '''no later than August 15'''. See Workshop registration form for further details.
*There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Agenda==

'''Day 1: Wednesday, September 3''' (Room: Irving 2 & 3)

8:30am - Registration and Continental Breakfast

9:00am - Opening remarks / Workshop goals (Richard Scheuermann)

9:15am - Session 1: Signs, symptoms and laboratory findings from a health care perspective (Scheuermann, moderator)

::: Combining clinical exam and laboratory findings in the rheumatology clinic (David Karp)
::: Clinical signs and symptoms in neonatology (Andrew James)

10:30am - Refreshment Break

10:45am - Session 2: Ontology approaches to describing the clinical phenotype (Smith, moderator)

::: PATO and Phenote: From model organism phenotypes to clinical medicine (Suzanna Lewis)
::: Reasoning with clinical exam and laboratory findings: The case of myocardial infarction (Sivaram Arabandi)

12:00pm - Buffet Lunch (Grand Prairie Room), '''Sponsored by:''' [http://www.leadhorsetech.com/LEAD_HORSE_TECHNOLOGIES/Home.html '''Lead Horse Technologies, Inc.''']

1:00pm - Session 3: Standardization of clinical and laboratory data in the context of clinical and translational research (Alan Ruttenberg, moderator)

::: Data standards from patient care to clinical and translational research: The CTSA perspective (Chris Chute)
::: Representation of clinical and laboratory findings in the CDISC SDTM (Bron Kisler)

3:00pm - Refreshment Break

3:30pm - Session 3 continued

::: The future of SNOMED-CT in the representation of clinical findings (Kent Spackman)
::: Problems with current approaches to clinical data (William Hogan)

5:30pm - Reception (Salons G & H)

'''Day 2: Thursday, September 4''' (Room: Irving 2 & 3)

8:30am - Continental Breakfast

9:00am - Session 4: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms (Bodenreider, moderator)

::: Laboratory data and metadata in laboratory information systems (Olivier Bodenreider and Anita Burgun)
::: An ontology-based approach for connecting disease pathogenesis with clinical/laboratory data (Richard Scheuermann)

10:30am - Refreshment Break

10:45am - Session 5: How consistent ontological design and development principles can lead to enhanced representation of signs, symptoms, and clinical and laboratory finding (Lewis, moderator)

12:00pm - Lunch Break

1:00pm - Session 6: Strategies to achieve convergence of ontologies, vocabularies and data structures in representing signs, symptoms, and clinical and laboratory findings (Scheuermann, moderator)

2:30pm - Refreshment Break

2:45pm - Session 6 (continued)

4:00pm - Close

==Confirmed Participants==

This is a working meeting and participation is restricted.

*Jonas Silva Almeida (MD Anderson Cancer Center / University of Texas)
*Sivaram Arabandi (Heart & Vascular Institute / Cleveland Clinic)
*John M. Armstrong (Lead Horse Technologies, Inc.)
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)
*Bruce Bray (Dept of Biomedical Informatics, University of Utah)
*Anita Burgun (Université de Rennes)
*Kei-Hoi Cheung (Senselab / Yale Center for Medical Informatics)
*Christopher G. Chute (National Center for Biomedical Ontology / Mayo Clinic)
*Paolo Ciccarese (Mass General Hospital / Harvard Medical School)
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)
*Gianluca Colombo (University of Milano-Bicocca, DISCo)
*Tommie G. Curtis (SAIC, NCICB Contractor)
*Amar K. Das (Center for Biomedical Informatics Research / Stanford University)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)
*William Hogan (University of Pittsburgh Medical Center)
*Zhang-Zhi Hu (PRO / Georgetown University Medical Center)
*Charles Jaffe (Health Level 7, Inc. (HL7))
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)
*David Karp (University of Texas Southwestern Medical Center at Dallas)
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)
*Pradeep Mutalik (Yale Center for Medical Informatics)
*Meredith L. Nahm (Duke Translational Medicine Institute)
*Chimezie Ogbuji (Cleveland Clinic Foundation)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)
*John Quinn (Health Level 7, Inc. (HL7))
*Alan Ruttenberg (Science Commons / Neurocommons)
*Neil Sarkar (Marine Biological Laboratory)
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)
*Kent A. Spackman (International Health Terminology Standards Development Organization)
*Larry Streepy (Cleveland Clinic Foundation)
*Nicole Washington (Lawrence Berkeley National Laboratory)
*Ashley Xia (NIAID / NIH)
*W. Jim Zheng (Biomedical Ontology Research Group / Medical University of South Carolina)

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

[http://bmir.stanford.edu/file_asset/index.php/1338/BMIR-2008-1302.pdf Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism], Samson W. Tu, Lakshika Tennakoon, Martin O'Connor, Ravi Shankar, and Amar Das.

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-07-30T13:31:02Z

Scheuerm: /* Tentative Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''
:[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas
:together with [http://ontology.buffalo.edu/smith/ Barry Smith], for the National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''
:[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]
:[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''
:September 3-4, 2008

''Venue:''
:Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
:Details with regard to discounted room rate will be sent to confirmed participants in due course.
:There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Tentative Agenda==

'''Day 1: Wednesday, September 3'''

8:30am Registration and Continental Breakfast

• Session 0 - Opening remarks

:: Richard Scheuermann (Dallas) - Workshop goals

• Session 1 - Signs, symptoms and laboratory findings from a health care perspective: The need for ontology

:: David Karp (Dallas)? - Combining clinical exam and laboratory findings in the rheumatology clinic
:: Andrew James (Toronto) - Clinical signs and symptoms in neonatology
:: Sivaram Arabandi (Cleveland) - Reasoning with clinical exam and laboratory findings: The Cleveland experience

12:00pm Lunch

• Session 2 - Standardization of clinical and laboratory data in the context of clinical and translational research - use cases, strategies and vision

:: Chris Chute (Rochester, MN)? - Data standards from patient care to clinical and translational research - the CTSA perspective
:: Bron Kisler (Austin)? - Representation of clinical and laboratory findings in the CDISC SDTM
:: Kent Spackman (IHTSDO, Portland) - The future of SNOMED-CT in the representation of clinical findings

'''Day 2: Thursday, September 4'''

8:30am Continental Breakfast

• Session 3 - Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms

:: William Hogan (Pittsburgh) - Problems with current approaches to clinical data
:: Olivier Bodenreider (Washington, D.C.) and Anita Burgun (Rennes)? - Laboratory data and metadata in laboratory information systems
:: Richard Scheuermann (Dallas) - An ontology-based approach for connecting disease pathogenesis with clinical/laboratory data

• Session 4 - Working session to utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory finding, and their interrelations

12:00 Lunch

• Session 5 - Crossing the genotype/phenotype divide: Discussion of strategies to achieve convergence between the ontological representation of disease signs and symptoms and clinical and laboratory findings with the existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities.

4:00pm Close

==Provisional List of Participants==

This is a working meeting and participation is restricted. Those wishing to communicate their interest in attending should contact Dr Richard Scheuermann [mailto:richard.scheuermann@utsouthwestern.edu] as soon as possible.

('''**''' = Registration form received)
*Jonas Silva Almeida (University of Texas MD Anderson Cancer Center)'''**'''
*Sivaram Arabandi (Cleveland Clinic Semantic Database for Cardiovascular Surgery)'''**'''
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Brian Athey (Center for Computational Medicine and Biology / Michigan)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)'''**'''
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)'''**'''
*Anita Burgun (Université de Rennes)'''**'''
*Helen Chen (Phillips)
*Kei Cheung (Senselab / Yale University)
*Christopher Chute (NCBO / Mayo Clinic)'''**'''
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)'''**'''
*Gianluca Colombo (University of Milano-Bicocca, DISCo)'''**'''
*Amar K. Das (Stanford Center for Biomedical Informatics Research)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)'''**'''
*Jeffrey S. Grethe (BIRN / University of California at San Diego)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Carol Hamilton (RTI International)
*William Hogan (University of Pittsburgh Medical Center)'''**'''
*Zhang-zhi Hu (PRO / Georgetown University Medical Center)'''**'''
*Charles Jaffe (HL7)
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)'''**'''
*David Karp (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)'''**'''
*Meredith L. Nahm (Duke Translational Medicine Institute)'''**'''
*Chimezie Ogbuji (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)'''**'''
*John Quinn (HL7)
*Dianne M. Reeves (NCI CBIIT / NIH)
*Alan Ruttenberg (Science Commons / Neurocommons)'''**'''
*Neil Sarkar (Marine Biological Laboratory, Woods Hole)'''**'''
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)'''**'''
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Kent A. Spackman (International Health Terminology Standards Development Organization)'''**'''
*Samson Tu (Stanford Center for Biomedical Informatics Research)
*Ashley Xia (NIAID / NIH)'''**'''
*W. Jim Zheng (Biomedical Ontology Research Group, Medical University of South Carolina)'''**'''

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-07-30T13:28:16Z

Scheuerm: /* Tentative Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''
:[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas
:together with [http://ontology.buffalo.edu/smith/ Barry Smith], for the National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''
:[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]
:[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''
:September 3-4, 2008

''Venue:''
:Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
:Details with regard to discounted room rate will be sent to confirmed participants in due course.
:There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Tentative Agenda==

'''Day 1: Wednesday, September 3'''

8:30am Registration and Continental Breakfast

• Session 0 - Opening remarks

:: Richard Scheuermann (Dallas) - Workshop goals

• Session 1 - Signs, symptoms and laboratory findings from a health care perspective: The need for ontology

:: David Karp (Dallas)? - Combining clinical exam and laboratory findings in the rheumatology clinic
:: Andrew James (Toronto) - Clinical signs and symptoms in neonatology
:: Sivaram Arabandi (Cleveland) - Reasoning with clinical exam and laboratory findings: The Cleveland experience

12:00pm Lunch

• Session 2 - Standardization of clinical and laboratory data in the context of clinical and translational research - use cases, strategies and vision

:: Chris Chute (Rochester, MN)? - Data standards from patient care to clinical and translational research - the CTSA perspective
:: Bron Kisler (Austin)? - Representation of clinical and laboratory findings in the CDISC SDTM
:: Kent Spackman (IHTSDO, Portland) - The future of SNOMED-CT in the representation of clinical findings

'''Day 2: Thursday, September 4'''

8:30am Continental Breakfast

• Session 3 - Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms

:: William Hogan (Pittsburgh) - Problems with current approaches to clinical data
:: Olivier Bodenreider (Washington, D.C.) and Anita Burgun (Rennes)? - Laboratory data and metadata in laboratory information systems
:: Richard Scheuermann (Dallas) - An ontology-based approach to describing disease pathogenesis and clinical/laboratory data

• Session 4 - Working session to utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory finding, and their interrelations

12:00 Lunch

• Session 5 - Crossing the genotype/phenotype divide: Discussion of strategies to achieve convergence between the ontological representation of disease signs and symptoms and clinical and laboratory findings with the existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities.

4:00pm Close

==Provisional List of Participants==

This is a working meeting and participation is restricted. Those wishing to communicate their interest in attending should contact Dr Richard Scheuermann [mailto:richard.scheuermann@utsouthwestern.edu] as soon as possible.

('''**''' = Registration form received)
*Jonas Silva Almeida (University of Texas MD Anderson Cancer Center)'''**'''
*Sivaram Arabandi (Cleveland Clinic Semantic Database for Cardiovascular Surgery)'''**'''
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Brian Athey (Center for Computational Medicine and Biology / Michigan)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)'''**'''
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)'''**'''
*Anita Burgun (Université de Rennes)'''**'''
*Helen Chen (Phillips)
*Kei Cheung (Senselab / Yale University)
*Christopher Chute (NCBO / Mayo Clinic)'''**'''
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)'''**'''
*Gianluca Colombo (University of Milano-Bicocca, DISCo)'''**'''
*Amar K. Das (Stanford Center for Biomedical Informatics Research)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)'''**'''
*Jeffrey S. Grethe (BIRN / University of California at San Diego)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Carol Hamilton (RTI International)
*William Hogan (University of Pittsburgh Medical Center)'''**'''
*Zhang-zhi Hu (PRO / Georgetown University Medical Center)'''**'''
*Charles Jaffe (HL7)
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)'''**'''
*David Karp (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)'''**'''
*Meredith L. Nahm (Duke Translational Medicine Institute)'''**'''
*Chimezie Ogbuji (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)'''**'''
*John Quinn (HL7)
*Dianne M. Reeves (NCI CBIIT / NIH)
*Alan Ruttenberg (Science Commons / Neurocommons)'''**'''
*Neil Sarkar (Marine Biological Laboratory, Woods Hole)'''**'''
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)'''**'''
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Kent A. Spackman (International Health Terminology Standards Development Organization)'''**'''
*Samson Tu (Stanford Center for Biomedical Informatics Research)
*Ashley Xia (NIAID / NIH)'''**'''
*W. Jim Zheng (Biomedical Ontology Research Group, Medical University of South Carolina)'''**'''

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-07-30T13:27:32Z

Scheuerm: /* Tentative Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''
:[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas
:together with [http://ontology.buffalo.edu/smith/ Barry Smith], for the National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''
:[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]
:[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''
:September 3-4, 2008

''Venue:''
:Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
:Details with regard to discounted room rate will be sent to confirmed participants in due course.
:There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Tentative Agenda==

'''Day 1: Wednesday, September 3'''

8:30am Registration and Continental Breakfast

• Session 0 - Signs, symptoms and laboratory findings from a health care perspective: The need for ontology

:: Richard Scheuermann (Dallas) - Workshop Goals

• Session 1 - Signs, symptoms and laboratory findings from a health care perspective: The need for ontology

:: David Karp (Dallas)? - Combining clinical exam and laboratory findings in the rheumatology clinic
:: Andrew James (Toronto) - Clinical signs and symptoms in neonatology
:: Sivaram Arabandi (Cleveland) - Reasoning with clinical exam and laboratory findings: The Cleveland experience

12:00pm Lunch

• Session 2 - Standardization of clinical and laboratory data in the context of clinical and translational research - use cases, strategies and vision

:: Chris Chute (Rochester, MN)? - Data standards from patient care to clinical and translational research - the CTSA perspective
:: Bron Kisler (Austin)? - Representation of clinical and laboratory findings in the CDISC SDTM
:: Kent Spackman (IHTSDO, Portland) - The future of SNOMED-CT in the representation of clinical findings

'''Day 2: Thursday, September 4'''

8:30am Continental Breakfast

• Session 3 - Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms

:: William Hogan (Pittsburgh) - Problems with current approaches to clinical data
:: Olivier Bodenreider (Washington, D.C.) and Anita Burgun (Rennes)? - Laboratory data and metadata in laboratory information systems
:: Richard Scheuermann (Dallas) - An ontology-based approach to describing disease pathogenesis and clinical/laboratory data

• Session 4 - Working session to utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory finding, and their interrelations

12:00 Lunch

• Session 5 - Crossing the genotype/phenotype divide: Discussion of strategies to achieve convergence between the ontological representation of disease signs and symptoms and clinical and laboratory findings with the existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities.

4:00pm Close

==Provisional List of Participants==

This is a working meeting and participation is restricted. Those wishing to communicate their interest in attending should contact Dr Richard Scheuermann [mailto:richard.scheuermann@utsouthwestern.edu] as soon as possible.

('''**''' = Registration form received)
*Jonas Silva Almeida (University of Texas MD Anderson Cancer Center)'''**'''
*Sivaram Arabandi (Cleveland Clinic Semantic Database for Cardiovascular Surgery)'''**'''
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Brian Athey (Center for Computational Medicine and Biology / Michigan)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)'''**'''
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)'''**'''
*Anita Burgun (Université de Rennes)'''**'''
*Helen Chen (Phillips)
*Kei Cheung (Senselab / Yale University)
*Christopher Chute (NCBO / Mayo Clinic)'''**'''
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)'''**'''
*Gianluca Colombo (University of Milano-Bicocca, DISCo)'''**'''
*Amar K. Das (Stanford Center for Biomedical Informatics Research)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)'''**'''
*Jeffrey S. Grethe (BIRN / University of California at San Diego)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Carol Hamilton (RTI International)
*William Hogan (University of Pittsburgh Medical Center)'''**'''
*Zhang-zhi Hu (PRO / Georgetown University Medical Center)'''**'''
*Charles Jaffe (HL7)
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)'''**'''
*David Karp (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Bron Kisler (CDISC)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)'''**'''
*Meredith L. Nahm (Duke Translational Medicine Institute)'''**'''
*Chimezie Ogbuji (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)'''**'''
*John Quinn (HL7)
*Dianne M. Reeves (NCI CBIIT / NIH)
*Alan Ruttenberg (Science Commons / Neurocommons)'''**'''
*Neil Sarkar (Marine Biological Laboratory, Woods Hole)'''**'''
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)'''**'''
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Kent A. Spackman (International Health Terminology Standards Development Organization)'''**'''
*Samson Tu (Stanford Center for Biomedical Informatics Research)
*Ashley Xia (NIAID / NIH)'''**'''
*W. Jim Zheng (Biomedical Ontology Research Group, Medical University of South Carolina)'''**'''

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

DallasWorkshop

2008-07-29T16:44:08Z

Scheuerm: /* Tentative Agenda */

==Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes==

''Workshop organized by:''
:[http://www.utsouthwestern.edu/findfac/research/0,2357,16416,00.html Richard Scheuermann], University of Texas Southwestern Medical Center, Dallas
:together with [http://ontology.buffalo.edu/smith/ Barry Smith], for the National Center for Biomedical Ontology / University at Buffalo

''Sponsored by:''
:[http://www.utsouthwestern.edu/utsw/home/home/research/ctsa University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program]
:[http://www.bioontology.org/ National Center for Biomedical Ontology (NCBO)]

''Date:''
:September 3-4, 2008

''Venue:''
:Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].
:Details with regard to discounted room rate will be sent to confirmed participants in due course.
:There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.

This workshop is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, with support from the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).

Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].

==Overview==

The aims of clinical and translational research are to achieve a better understanding of the pathogenesis of human disease in order to develop effective diagnostic, therapeutic and prevention strategies. Biomedical informatics can play an important role is supporting this research by facilitating the management, integration, analysis and exchange of data derived from and related to the research problems being studied. A key aspect of this support is to bring clarity, rigor and formalism to the representation of

::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and

::2. the interrelations between these distinct entities both in patient management and in clinical research,

thus allowing the data to be more readily retrievable and shareable, and more able to serve in the support of algorithmic reasoning.

==Goals==

The tentative goals of the workshop will be to:

*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.

*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.

*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.

*Take first steps towards harmonizing the ontological representation of disease signs and symptoms and clinical and laboratory findings with existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework

==Provisional List of Participants==

This is a working meeting and participation is restricted. Those wishing to communicate their interest in attending should contact Dr Richard Scheuermann [mailto:richard.scheuermann@utsouthwestern.edu] as soon as possible.

('''**''' = Registration form received)
*Jonas Silva Almeida (University of Texas MD Anderson Cancer Center)
*Sivaram Arabandi (Cleveland Clinic Semantic Database for Cardiovascular Surgery)'''**'''
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Brian Athey (Center for Computational Medicine and Biology / Michigan)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)'''**'''
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)'''**'''
*Anita Burgun (Université de Rennes)'''**'''
*Helen Chen (Phillips)
*Kei Cheung (Senselab / Yale University)
*Christopher Chute (NCBO / Mayo Clinic)'''**'''
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)'''**'''
*Gianluca Colombo (University of Milano-Bicocca, DISCo)'''**'''
*Amar K. Das (Stanford Center for Biomedical Informatics Research)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)'''**'''
*Jeffrey S. Grethe (BIRN / University of California at San Diego)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Carol Hamilton (RTI International)
*William Hogan (University of Pittsburgh Medical Center)'''**'''
*Zhang-zhi Hu (PRO / Georgetown University Medical Center)'''**'''
*Charles Jaffe (HL7)
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)'''**'''
*David Karp (University of Texas Southwestern Medical Center at Dallas)'''**'''
*Bron Kisler (CDISC)
*Harold Lehmann (John Hopkins Medical Institutions)
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)'''**'''
*Meredith L. Nahm (Duke Translational Medicine Institute)'''**'''
*Chimezie Ogbuji (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)'''**'''
*John Quinn (HL7)
*Dianne M. Reeves (NCI CBIIT / NIH)
*Alan Ruttenberg (Science Commons / Neurocommons)'''**'''
*Neil Sarkar (Marine Biological Laboratory, Woods Hole)
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)'''**'''
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)'''**'''
*Kent A. Spackman (International Health Terminology Standards Development Organization)'''**'''
*Samson Tu (Stanford Center for Biomedical Informatics Research)
*Ashley Xia (NIAID / NIH)'''**'''
*W. Jim Zheng (Biomedical Ontology Research Group, Medical University of South Carolina)'''**'''

In addition to NCBO and the University of Texas Southwestern Medical Center, it is our goal to have the following communities represented: CTSA, HL7, CDISC, SNOMED, and OBO, as well as the NIH.

==Tentative Agenda==

'''Day 1: Wednesday, September 3'''

8:30am Registration and Continental Breakfast

• Session 1 - Representation of sign, symptoms and laboratory findings from a health care perspective
:: Andrew James (Toronto)? - Clinical exam signs and symptoms in neonatology
:: David Karp (Dallas)? - Combining clincal exam and laboratory findings in the Rheumatology clinic
:: Sivaram Arabandi (Cleveland)? - Signs and symptoms of infectious diseases

• Session 2 - Standardized treatment of clinical and laboratory data in the context of clinical research - use cases, strategies and vision
:: Chris Chute (Rochester, MN)? - Data standards from patient care to clinical research - the CTSA perspective
:: Bron Kisler (Austin)? - Clinical and laboratory finding representation in the CDISC SDTM
:: Kent Spackman (Portland)? - Use of SNOMED-CT findings-related terms in support of clinical research

'''Day 2: Thursday, September 4'''

8:30am Continental Breakfast

• Session 3 - Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms
:: Richard Scheuermann (Dallas)? - An ontology-based approach for describing the semantic relationships between disease pathogenesis and clinical/laboratory findings
:: Olivier Bodenreider (Washington, D.C.)? - Laboratory data and metadata in laboratory information systems

• Session 4 - Working session to utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory finding, and their interrelations

• Session 5 - Discussion of strategies to achieve convergence between the ontological representation of disease signs and symptoms and clinical and laboratory findings with the existing and emerging standards in knowledge representation from the health informatics and bioinformatics communities

4:00pm Close

==Suggested Background Reading==

[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf OBO Foundry]: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

[http://www.biomedcentral.com/1471-2105/9/S4/S3 Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource

==Useful Links==

[http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype Mammalian Phenotype Ontology]

[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]

[http://obofoundry.org OBO Foundry]

[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]

Upcoming Meetings

2007-09-25T17:39:46Z

Scheuerm:

Go back to [[OCI:Main Page]]

'''May 16-17, 2007'''

[[Workshop on Clinical Trial Ontology]], Bethesda, MD

'''October 2-3, 2007'''

[[2007 CDISC International Interchange]], Bethesda, MD
[[Image:Scheuermann_CDISC_presentation_part1.ppt‎]]
[[Image:Scheuermann_CDISC_presentation_part2.ppt‎]]
[[Image:Scheuermann_CDISC_presentation_part3.ppt‎]]
[[Image:Scheuermann_CDISC_presentation_part4.ppt‎]]

Upcoming Meetings

2007-09-25T17:39:02Z

Scheuerm:

Go back to [[OCI:Main Page]]

'''May 16-17, 2007'''

[[Workshop on Clinical Trial Ontology]], Bethesda, MD

'''October 2-3, 2007'''

[[2007 CDISC International Interchange]], Bethesda, MD
[[File:Scheuermann_CDISC_presentation_part1.ppt‎]]
[[File:Scheuermann_CDISC_presentation_part2.ppt‎]]
[[File:Scheuermann_CDISC_presentation_part3.ppt‎]]
[[File:Scheuermann_CDISC_presentation_part4.ppt‎]]

Upcoming Meetings

2007-09-25T17:36:35Z

Scheuerm:

Upcoming Meetings

2007-09-25T17:35:56Z

Scheuerm:

File:Scheuermann CDISC presentation part4.ppt

2007-09-25T17:34:35Z

Scheuerm:

File:Scheuermann CDISC presentation part3.ppt

2007-09-25T17:34:12Z

Scheuerm:

File:Scheuermann CDISC presentation part2.ppt

2007-09-25T17:32:27Z

Scheuerm:

File:Scheuermann CDISC presentation part1.ppt

2007-09-25T17:30:08Z

Scheuerm:

Upcoming Meetings

2007-09-25T17:24:53Z

Scheuerm:

Go back to [[OCI:Main Page]]

'''May 16-17, 2007'''

[[Workshop on Clinical Trial Ontology]], Bethesda, MD

'''October 2-3, 2007'''

[[2007 CDISC International Interchange]], Bethesda, MD

OCI:Main Page

2007-09-13T15:53:16Z

Scheuerm: /* Conference Call Information */

=OCI - Ontology for Clinical Investigations=

==About OCI==

The goal of the OCI Working Group 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.

==Recent Developments==

==Conference Call Information==
* '''Next OCI conference call: Thursday, September 13 at 11am CDT.'''
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[OCI WG Chairs]]
* [[OCI Curators]]
* [[Other members of OCI WG]]

==Draft version of OCI==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[OCI Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==OCI Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[OCI Check-out Procedure Policy]]
* [[OCI Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==OCI Wiki information==

Minutes from 08/30/07 Conference Call

2007-09-04T21:26:27Z

Scheuerm:

Go back to [[OCI:Main Page]]

Present on the call: Jim Zheng, Wenle Zhao, Jennifer Fostel, Richard Scheuermann 

1. Upcoming CDISC presentation - The OCI abstract was accepted for an oral presentation at the upcoming [http://www.cdisc.org/events/index.html 2007 CDISC International Interchange] on October 1-5 2007 at the Marriott Bethesda North Hotel & Conference Center. 

'''ACTION ITEM:''' A draft presentation will assembled by Richard and distributed for comments by the OCI Working Group in mid-September. 

2. Richard discussed the need for use cases to demonstrate both how the OCI ontology would be used in the clinical research domain and how we would demonstrate that using an ontology versus a flat vocabulary would add value to clinical research representation and analysis. All parties were asked to consider this issue for discussion at the next OCI conference call.

3. Jim presented an overview of his analysis of the OCI term list using his abstract analysis algorithm. This algorithm looks for overrepresentation of specific terms in a subset of selected Pubmed abstracts, in this case the subset of abstracts containing the term "clinical trials". For the most part, terms in the OCI list were overrepresented in these abstracts suggesting that they are indeed specific for the clinical trials domain. The list was further evaluated by Wenle as a subjective assessment of relevance by a domain expert. 

'''ACTION ITEM:''' Jim will merge these data with the analysis of OBI branch membership for the same terms developed previously by Jennifer. The merged list will be used to establish priority for future OCI term work. 

4. The possibility of obtaining external funding to support OCI development work was discussed, including a recent RFA released by the NIH entitled [http://grants.nih.gov/grants/guide/pa-files/PAR-07-425.html Data Ontologies for Biomedical Research]. 

'''ACTION ITEM:''' Jim was encouraged to explore the details of this funding opportunity further. 

Next call scheduled for September 13th.

Minutes from 08/30/07 Conference Call

2007-09-04T21:21:01Z

Scheuerm: New page: Go back to OCI:Main Page Present on the call: Jim Zheng, Wenle Zhao, Jennifer Fostel, Richard Scheuermann 1. Upcoming CDISC presentation - The OCI abstract was accepted for an o...

Go back to [[OCI:Main Page]]

Present on the call: Jim Zheng, Wenle Zhao, Jennifer Fostel, Richard Scheuermann 

1. Upcoming CDISC presentation - The OCI abstract was accepted for an oral presentation at the upcoming [http://www.cdisc.org/events/index.html 2007 CDISC International Interchange] on October 1-5 2007 at the Marriott Bethesda North Hotel & Conference Center. 

'''ACTION ITEM:''' A draft presentation will assembled by Richard and distributed for comments by the OCI Working Group in mid-September. 

2. Jim presented an overview of his analysis of the OCI term list using his abstract analysis algorithm. This algorithm looks for overrepresentation of specific terms in a subset of selected Pubmed abstracts, in this case the subset of abstracts containing the term "clinical trials". For the most part, terms in the OCI list were overrepresented in these abstracts suggesting that they are indeed specific for the clinical trials domain. The list was further evaluated by Wenle as a subjective assessment of relevance by a domain expert. 

'''ACTION ITEM:''' Jim will merge these data with the analysis of OBI branch membership for the same terms developed previously by Jennifer. The merged list will be used to establish priority for future OCI term work. 

3. The possibility of obtaining external funding to support OCI development work was discussed, including a recent RFA released by the NIH entitled [http://grants.nih.gov/grants/guide/pa-files/PAR-07-425.html Data Ontologies for Biomedical Research]. 

'''ACTION ITEM:''' Jim was encouraged to explore the details of this funding opportunity further. 

Next call scheduled for September 13th.

Conference Call Minutes

2007-09-04T20:55:01Z

Scheuerm:

Go back to [[OCI:Main Page]]

* [[Minutes from 08/30/07 Conference Call]]
* [[Minutes from 08/10/07 Conference Call]]
* [[Minutes from 08/02/07 Conference Call]]
* [[Minutes from 07/19/07 Conference Call]]
* [[Minutes from 06/28/07 Conference Call]]
* [[Minutes from 05/10/07 Conference Call]]
* [[Minutes from 05/03/07 Conference Call]]
* [[Minutes from 04/19/07 Conference Call]]
* [[Minutes from 04/12/07 Conference Call]]

OCI:Main Page

2007-09-04T20:53:17Z

Scheuerm: /* OCI - Ontology of Clinical Investigation */

=OCI - Ontology for Clinical Investigations=

==About OCI==

The goal of the OCI Working Group 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.

==Recent Developments==

==Conference Call Information==
* '''Next OCI conference call: Friday, August 10 at 11am CDT.'''
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[OCI WG Chairs]]
* [[OCI Curators]]
* [[Other members of OCI WG]]

==Draft version of OCI==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[OCI Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==OCI Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[OCI Check-out Procedure Policy]]
* [[OCI Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==OCI Wiki information==

Conference Call Schedule

2007-08-09T13:48:56Z

Scheuerm:

Go back to [[OCI:Main Page]]

'''Meeting changes'''
*NO CALL on Thursday, April 26, 2007. Action items to be accomplished via wiki and email.
*NO CALL on Thursday, July 12, 2007 (OBI meeting).
*ADDED CALL on Friday, August 10, 2007 at 12:00 noon EDT. Doug Fridsma will be presenting an overview of BRIDG.

'''Scheduled meetings:'''
*BIWEEKLY (every other Thursday) starting August 2, 2007 at 9:00am PST, 11:00am CST, noon EST, 6:00pm Germany

Conference Call Agendas

2007-08-01T21:17:27Z

Scheuerm: /* Conference Call Agendas */

Go back to [[OCI:Main Page]]

= Conference Call Agendas =

==August 2==
1. Overview of the CDISC Terminology project by Bron Kisler 
2. Brief review of Jim Zhengs text mining approach for identifying clinical terms from clinical protocols 

==May 10==
1. Review the recent work that several people have added 
2. Review the goals and organization of the workshop 
3. Discuss how we think the CTO could be useful (use cases) 

==May 3==
*Discussion of High-Level BFO-OBI Structure
*Discussion of new added terms
*Plans for CTO Workshop
*Action items for the coming week

==April 19==
'''1. Ontology of Biomedical Investigation'''
*a. Overview of OBI core (Fostel, tentative)
'''2. CTO development approach (with deadlines and milestones)'''
*a. Goals for completion by May16th
*b. Status of proposed steps
**term list assembly
**term list merging
**term positioning into branches
**term CTO definition
'''3. High-level concept branches'''

'''4. Others'''

==April 12==
'''1. CTO Working Group (WG) Organization'''
*a. Are current assignments acceptable?
*b. Need a secretary
*c. Responsibilities
*d. Schedule of calls
'''2. Development and WG policies in general'''
*a. Draft metadata and CTO check-out policies
*b. CTO WG membership policy
'''3. Ontology Organization'''
*a. Relationship with the BFO
*b. Relationship with the OBI
'''4. CTO scope'''
*a. Definition of the CTO domain
*b. Relationship with other ontologies
'''5. CTO development approach (with deadlines and milestones)'''
*a. Proposed steps
**term list assembly
**term list merging
**term positioning into branches
**term CTO definition
*b. Goals for completion by May 16th
*c. Managing discussion threads
'''6. Information objects as dependent continuants (if time)'''

OCI:Main Page

2007-08-01T21:14:36Z

Scheuerm: /* Conference Call Information */

=OCI - Ontology of Clinical Investigation=

==About OCI==

The goal of the OCI Working Group 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.

==Recent Developments==

==Conference Call Information==
* '''Next OCI conference call: Thursday, August 2.'''
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[OCI WG Chairs]]
* [[OCI Curators]]
* [[Other members of OCI WG]]

==Draft version of OCI==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[OCI Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==OCI Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[OCI Check-out Procedure Policy]]
* [[OCI Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==OCI Wiki information==

Other members of OCI WG

2007-07-10T13:39:03Z

Scheuerm:

Go back to [[OCI:Main Page]]

* [[Matthias Brochhausen]]
* [[Amar K. Das]]
* [[Dave Parrish]]
* [[Kirsten Forsberg]]
* [[Matthias Samwald]]
* [[Barry Smith]]

Workshop on Clinical Trial Ontology

2007-05-30T22:35:32Z

Scheuerm: /* '''Agenda''' */

== '''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 [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:

(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 [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>Wednesday, May 16 - Building 45 (Natcher), Balcony A</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>Thursday, May 17 - Building 31, Conference Room 10</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:

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: [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) ==

[http://cto.googlecode.com/svn/trunk/CTO.owl Current OWL version]

[[Image:CTO.jpg]]

Workshop on Clinical Trial Ontology

2007-05-30T22:30:01Z

Scheuerm: /* '''Agenda''' */

== '''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 [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:

(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 [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>Wednesday, May 16 - Building 45 (Natcher), Balcony A</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>Thursday, May 17 - Building 31, Conference Room 10</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 [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:

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: [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) ==

[http://cto.googlecode.com/svn/trunk/CTO.owl Current OWL version]

[[Image:CTO.jpg]]

File:CTO Workshop Day 2 RS JL.doc

2007-05-30T22:28:04Z

Scheuerm:

Action items from 05/03/07 call

2007-05-03T17:55:52Z

Scheuerm:

Go back to [[CTO:Main Page]]

*Review term lists and Jennifer’s shot at placing terms into OBI categories (download the May 3 excel file to manipulate the term lists and add your comments).

*Re-generate OBI schematic based on current OBI version and come up with a permanent way to accurately synchronize the schematic with the current OBI draft.

*Richard will send out email about upcoming workshop, including issues that need to be addressed (such as how we want others to contribute to CTO developoment in a controlled fashion), what we should present, and what we want to accomplish (especially on Day 2).

High-level Concepts v0.2

2007-05-02T19:09:01Z

Scheuerm: /* High-Level Concepts version 0.2 */

Go back to [[CTO:Main Page]]

==High-Level Concepts version 0.2==
Initial High-level Concepts in black font

Additions from Simona in blue font

Additions from Richard in green font
*Events
*Periods
**Study phases
**Protocol phases
*Sequence of events
*Study designs
**Descriptive research – research in which the investigator attempts to describe a group of individuals based on a set of variable in order to document their characteristics
***Case study – description of one or more patients
***Developmental research – description of pattern of change over time
***Normative research – establishing normal values
***Qualitative research – gathering data through interview or observation
***Evaluation research – objectively assess a program or policy by describing the needs for the services or policy, often using surveys or questionaires
**Exploratory research
***Cohort or case-control studies – establish associations through epidemiological studies
***Methodological studies – establish reliability and validity of a new method
***Secondary analysis – exploring new relationships in old data
***Historical research – reconstructing the past through an assessment of archives or other records
**Experimental research
***Randomized clinical trial – controlled comparison of an experimental intervention allowing the assessment of the causes of outcomes
****Single-subject design
****Sequential clinical trial
****Evaluation research – assessment of the success of a program or policy
***Quasi-experimental research
***Meta-analysis – statistically combining findings from several different studies to obtain a summary analysis

*Research types
**Randomized Clinical Trial
*Methods
*Stakeholders
**Participants
**Investigators
**Monitors
***Study committee
**Sponsors
*Populations
**Recruited population
***Randomized population
***Enrolled population
***Eligible population
***Screened population

**Excluded population
***Excluded postrandomization population
***Not-randomized-population
***Not-enrolled-population
***Not-eligible-population

**Analyzed-population
***All subjects
***Study arm population
***Crossover population
***Subgroup population

*Variables
**Independent variable
***Intervention
****Procedure
****Device implantation
****Drug treatment
****Placebo treatment
****Sham procedure
****Usual care
****Counseling
***Cointervention

**Dependent variable (responding variable)
***Outcome
****Primary outcome
****Secondary outcome
****Adverse event/Side effect
****Ancillary outcome

*Digital and paper artifacts
*Protocol
**Intended protocol
**Executed protocol
**Protocol change

*Protocol application
**Assessments
***Experimental assays
***Observations
****Physical exam
***Interview
***Self-assessments
**Data analysis
***Data partitioning
***Data transformation
***Data pooling
***Data summarization
***Reliability
***Correlation
**Specimen processing
***Procurement
***Specimen partitioning/purification
***Specimen storage
**Treatment assignment
**Blinding
**Follow-up

*Measurement scale
**Nominal
**Ordinal
**Interval
**Ratio
*Participant characteristic (phenotype)
**Baseline characteristic

----

==High-Level Structure from BFO-OBI==

[[Image:High Level BFO_OBI.jpg]]

High-level Concepts v0.2

2007-05-01T22:02:21Z

Scheuerm: /* High-Level Concepts version 0.2 */

==High-Level Concepts version 0.2==
Initial High-level Concepts in black font

Additions from Simona in blue font

Additions from Richard in green font
*Events
*Periods
**Study phases
**Protocol phases
*Sequence of events
*Study designs
**Descriptive research – research in which the investigator attempts to describe a group of individuals based on a set of variable in order to document their characteristics
***Case study – description of one or more patients
***Developmental research – description of pattern of change over time
***Normative research – establishing normal values
***Qualitative research – gathering data through interview or observation
***Evaluation research – objectively assess a program or policy by describing the needs for the services or policy, often using surveys or questionaires
**Exploratory research
***Cohort or case-control studies – establish associations through epidemiological studies
***Methodological studies – establish reliability and validity of a new method
***Secondary analysis – exploring new relationships in old data
***Historical research – reconstructing the past through an assessment of archives or other records
**Experimental research
***Randomized clinical trial – controlled comparison of an experimental intervention allowing the assessment of the causes of outcomes
****Single-subject design
****Sequential clinical trial
****Evaluation research – assessment of the success of a program or policy
***Quasi-experimental research
***Meta-analysis – statistically combining findings from several different studies to obtain a summary analysis

*Research types
**Randomized Clinical Trial
*Methods
*Stakeholders
**Participants
**Investigators
**Monitors
**Sponsors
*Populations
**Screened population
**Recruited population
**Eligible population
**Enrolled population
**Randomized population
**Analysed population
**Crossover population
**Subgroup population
*Variables
**Independent variable
***Intervention
****Procedure
****Device implantation
****Drug treatment
****Placebo treatment
****Sham procedure
****Usual care
****Counseling
***Cointervention
**Dependent variable (responding variable)
***Outcome
****Primary outcome
****Secondary outcome
****Adverse event/Side effect
****Ancillary outcome
*Digital and paper artifacts
*Protocol
**Intended protocol
**Executed protocol
*Protocol application
**Assessments
***Experimental assays
***Observations
****Physical exam
***Interview
***Self-assessments
**Data analysis
***Data partitioning
***Data transformation
***Data pooling
***Data summarization
***Reliability
***Correlation
**Specimen processing
***Procurement
***Specimen partitioning/purification
***Specimen storage
*Measurement scale
**Nominal
**Ordinal
**Interval
**Ratio
*Participant characteristic (phenotype)
**Baseline characteristic

----
==High-Level Structure from BFO-OBI==

[[Image:High Level BFO_OBI.jpg]]

High-level Concepts v0.2

2007-05-01T20:27:30Z

Scheuerm: /* High-Level Concepts */

High-level Concepts v0.2

2007-05-01T20:04:47Z

Scheuerm: New page: ==High-Level Concepts== *Events *Periods **Study phases **Protocol phases *Sequence of events *Study designs *Research types **Randomized Clinical Trial *M...

==High-Level Concepts==
*Events
*Periods
**Study phases
**Protocol phases
*Sequence of events
*Study designs
*Research types
**Randomized Clinical Trial
*Methods
*Stakeholders
**Participants
**Investigators
**Monitors
**Sponsors
*Populations
**Screened population
**Recruited population
**Eligible population
**Enrolled population
**Randomized population
**Analysed population
**Crossover population
**Subgroup population
*Variables
**Independent variable
***Intervention
****Procedure
****Device implantation
****Drug treatment
****Placebo treatment
****Sham procedure
****Usual care
****Counseling
***Cointervention
**Dependent variable (responding variable)
***Outcome
****Primary outcome
****Secondary outcome
****Adverse event/Side effect
****Ancillary outcome
*Digital and paper artifacts
*Protocol
**Intended protocol
**Executed protocol
*Protocol application
**Assessments
***Experimental assays
***Observations
****Physical exam
***Interview
***Self-assessments
**Data analysis
***Data partitioning
***Data transformation
***Data pooling
***Data summarization
***Reliability
***Correlation
**Specimen processing
***Procurement
***Specimen partitioning/purification
***Specimen storage
*Measurement scale
**Nominal
**Ordinal
**Interval
**Ratio
*Participant characteristic (phenotype)
**Baseline characteristic

OCI:Main Page

2007-05-01T20:04:33Z

Scheuerm: /* Ontology Development Items */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[CTO Check-out Procedure Policy]]
* [[CTO Working Group Membership Policy]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

High-level Concepts

2007-05-01T15:47:42Z

Scheuerm: /* High-Level Concepts */

Go back to [[CTO:Main Page]]

==High-Level Concepts==
*Events
*Periods
**Study phases
**Protocol phases
*Sequence of events
*Study designs
*Research types
*Methods
*Stakeholders
**Participants
**Investigators
**Monitors
**Sponsors
*Populations
*Variables
**Independent variable
**Dependent variable (responding variable)
***Outcome
*Digital and paper artifacts
*Protocol
*Protocol application
**Assessments
***Experimental assays
***Observations
****Physical exam
***Interview
***Self-assessments
**Data analysis
***Data partitioning
***Data transformation
***Data pooling
***Data summarization
***Reliability
***Correlation
**Specimen processing
***Procurement
***Specimen partitioning/purification
***Specimen storage
*Measurement scale
**Nominal
**Ordinal
**Interval
**Ratio
*Participant characteristic (phenotype)

----

==High-Level Structure from BFO-OBI==

[[Image:High Level BFO_OBI.jpg]]

File:High Level BFO OBI.jpg

2007-05-01T15:46:04Z

Scheuerm:

OCI Check-out Procedure Policy

2007-04-18T17:56:58Z

Scheuerm: New page: [Adapted from Cristian Cocos (username: Aqualung)] When planning to work on the ontology: 1. Make sure, via Skype, that no one is working on the ontology right now, so that you can be cer...

[Adapted from Cristian Cocos (username: Aqualung)] When planning to work on the ontology:

1. Make sure, via Skype, that no one is working on the ontology right now,
so that you can be certain that the ontology you will be downloading is the
latest version.

2. Let everybody know that you will be working on the ontology for a certain amount of time, starting now. (Offline Skype status, or no reply, will be interpreted as "not working on the ontology, go ahead"! Make sure, then, that you are always online when working on the CTO.)

3. Download the latest CTO version using your SVN client.

4. Read the log, just so you know what has happened to the CTO since you last
updated it.

5. Do your work, keeping track religiously of all the changes you make. All of
this will go into the log. Will be making heavy use of abbreviations
(ac=added class, mc=modified class, dc=deleted class etc.). The log should
be as exhaustive as possible.

6. When done, you should save all changes locally, and upload them onto the server.
Make sure you fill out the log when uploading (you will be prompted to do
that at the time of the upload).

7. Let everyone know via Skype that you have just uploaded the latest
version, and that you are done with the CTO for now.

Ontology Metadata Policy (from OBI)

2007-04-18T17:56:04Z

Scheuerm: New page: '''Minimal requirement for term annotations in the CTO (metadata)''' Mandatory metadata: MUST be provided *preferred_term: The concise, meaningful, and human-friendly name for a class or...

'''Minimal requirement for term annotations in the CTO (metadata)'''

Mandatory metadata: MUST be provided
*preferred_term: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
*definition: The official CTO definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with informal examples to further clarify the meaning of the term.
*definition_editor: The name of the editor of the definition.
*definition_source: An unambiguous and traceable reference to the source of the definition. Examples: ISBN, URI plus date, MeSH Term, PUBMED ID, DOI.
*curation_status: The curation status of a class or property. The allowed values come from an enumerated list of predefined terms. Examples: raw import, obo definition incomplete, graph position temporary, uncurated, curation approved
*example: A phrase describing how a term should be used. May also include other kinds of examples, such as widely known subclasses or instances of the class.
Optional metadata: SHOULD be provided
*alternative_term: An alternative name for a class or property which means the same thing, i.e. semantically equivalent, as the preferred_term.
*alternative_term_tag: A tag to indicate sets of alternative terms. Examples: toxicogenomics_community, abbreviation.
*alternative_term_source: An unambiguous and traceable reference to the source of the alternative_term. Examples: ISBN, URI plus date, MeSH Term, PUBMED ID, DOI.
*editor_note: An administrative note intended for the editor. It will not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
*external_class: An annotation property that indicates external classes, including their subtrees, for a given anchor class.

OCI:Main Page

2007-04-18T17:54:32Z

Scheuerm: /* CTO Development Policies */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[CTO Check-out Procedure Policy]]
* [[CTO Working Group Membership Policy]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

OCI Working Group Membership Policy

2007-04-18T17:53:21Z

Scheuerm: New page: '''To be developed'''

'''To be developed'''

OCI:Main Page

2007-04-18T17:53:01Z

Scheuerm: /* CTO Development Policies */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]
* [[CTO Working Group Membership Policy]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

High-level Concepts

2007-04-18T17:50:47Z

Scheuerm:

==High-Level Concepts==
*Events
*Periods
**Study phases
**Protocol phases
*Sequence of events
*Study designs
*Research types
*Methods
*Stakeholders
**Participants
**Investigators
**Monitors
**Sponsors
*Populations
*Variables
**Independent variable
**Dependent variable (responding variable)
***Outcome
*Digital and paper artifacts
*Protocol
*Protocol application
**Assessments
***Experimental assays
***Observations
****Physical exam
***Interview
***Self-assessments
**Data analysis
***Data partitioning
***Data transformation
***Data pooling
***Data summarization
***Reliability
***Correlation
**Specimen processing
***Procurement
***Specimen partitioning/purification
***Specimen storage
*Measurement scale
**Nominal
**Ordinal
**Interval
**Ratio
*Participant characteristic (phenotype)

Conference Call Agendas

2007-04-18T17:44:00Z

Scheuerm: /* April 19 */

= Conference Call Agendas =
==April 12==
'''1. CTO Working Group (WG) Organization'''
*a. Are current assignments acceptable?
*b. Need a secretary
*c. Responsibilities
*d. Schedule of calls
'''2. Development and WG policies in general'''
*a. Draft metadata and CTO check-out policies
*b. CTO WG membership policy
'''3. Ontology Organization'''
*a. Relationship with the BFO
*b. Relationship with the OBI
'''4. CTO scope'''
*a. Definition of the CTO domain
*b. Relationship with other ontologies
'''5. CTO development approach (with deadlines and milestones)'''
*a. Proposed steps
**term list assembly
**term list merging
**term positioning into branches
**term CTO definition
*b. Goals for completion by May 16th
*c. Managing discussion threads
'''6. Information objects as dependent continuants (if time)'''

==April 19==
'''1. Ontology of Biomedical Investigation'''
*a. Overview of OBI core (Fostel, tentative)
'''2. CTO development approach (with deadlines and milestones)'''
*a. Goals for completion by May16th
*b. Status of proposed steps
**term list assembly
**term list merging
**term positioning into branches
**term CTO definition
'''3. High-level concept branches'''

'''4. Others'''

High-level Concepts

2007-04-18T17:43:22Z

Scheuerm: New page: Events Periods Study phases Protocol phases Sequence of events Study designs Research types Methods Stakeholders Participants Investigators Monitors Sponsors Population...

Events
Periods
Study phases
Protocol phases
Sequence of events
Study designs
Research types
Methods
Stakeholders
Participants
Investigators
Monitors
Sponsors
Populations
Variables
Independent variable
Dependent variable (responding variable)
outcome
Digital and paper artifacts
Protocol
Protocol application
Assessments
Experimental assays
Observations
Physical exam
Interview
Self-assessments
Data analysis
Data partitioning
Data transformation
Data pooling
Data summarization
Reliability
Correlation
Specimen processing
Procurement
Specimen partitioning/purification
Specimen storage
Measurement scale
Nominal
Ordinal
Interval
Ratio
Participant characteristic (phenotype)

OCI:Main Page

2007-04-18T17:43:07Z

Scheuerm: /* Ontology Development Items */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

High-level Term List

2007-04-18T17:42:23Z

Scheuerm: New page: Events Periods Study phases Protocol phases Sequence of events Study designs Research types Methods Stakeholders Participants Investigators Monitors Sponsors Population...

OCI:Main Page

2007-04-18T17:41:24Z

Scheuerm: /* Ontology Development Items */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Term List]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==