Difference between revisions of "DallasWorkshop"

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''Workshop organized by:''  
 
''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
+
[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:''  
 
''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.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:''  
 
''Date:''  
:September 3-4, 2008
+
 
 +
September 3-4, 2008
 +
 
 +
 
  
 
''Venue:''  
 
''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.
+
Dallas/Fort Worth Airport Marriott [http://www.marriott.com/hotels/travel/dfwap-dallas-fort-worth-airport-marriott/].  
:There is no participation fee. Continental breakfast and refreshments will be provided to all registered participants at no cost.
+
*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).  
 
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).  
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==Overview==
 
==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  
+
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 in 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  
 
::1. disease initiation, progression, pathogenesis, signs, symptoms, assessments, clinical and laboratory findings, disease diagnosis, treatment, treatment response and outcome, and  
Line 34: Line 48:
 
==Goals==
 
==Goals==
  
The tentative goals of the workshop will be to:
+
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 I-III, Lobby Level)
 +
 
 +
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 [http://ontology.buffalo.edu/08/phenotype/karp.ppt slides] (David Karp)
 +
::: Clinical signs and findings in neonatology [http://ontology.buffalo.edu/08/phenotype/JAMES.ppt slides] (Andrew James)
 +
 
 +
10:30am - Refreshment Break
 +
 
 +
10:45am - Session 2: Ontology approaches to describing the clinical phenotype [http://ontology.buffalo.edu/08/phenotype/SMITH.ppt slides] (Smith, moderator)
 +
 
 +
::: Reasoning with clinical exam and laboratory findings: The case of myocardial infarction [http://ontology.buffalo.edu/08/phenotype/ARABANDI.pdf slides] (Sivaram Arabandi)
  
*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.
+
12:00pm - Buffet Lunch (Arlington Room, Lower Level), '''''Provided by the generous support of''''' [http://www.leadhorsetech.com/LEAD_HORSE_TECHNOLOGIES/Home.html '''''Lead Horse Technologies, Inc.''''']
  
*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.
+
1:00pm - Session 3: Standardization of clinical and laboratory data in the context of clinical and translational research (Jaffe, moderator)
  
*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.
+
::: Data standards from patient care to clinical and translational research: The CTSA perspective [http://ontology.buffalo.edu/08/phenotype/CHUTE.ppt slides] (Chris Chute)
 +
::: Representation of clinical and laboratory findings in the CDISC SDTM [http://ontology.buffalo.edu/08/phenotype/KISLER-WALKER.ppt slides] (Bron Kisler and Gary Walker)
  
*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
+
3:00pm - Refreshment Break
  
*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework
+
3:30pm - Session 3 continued (Ruttenberg, moderator)
  
==Tentative Agenda==
+
::: The future of SNOMED-CT in the representation of clinical findings [http://ontology.buffalo.edu/08/phenotype/SPACKMAN.ppt slides] (Kent Spackman)
 +
:::      Problems with current approaches to clinical data [http://ontology.buffalo.edu/08/phenotype/HOGAN.ppt slides] (William Hogan)
  
'''Day 1: Wednesday, September 3'''
+
5:30pm - Reception (Grand Prairie Room, Lower Level), '''''Provided by the generous support of The Cleveland Clinic Foundation SemanticDB'''''
  
8:30am Registration and Continental Breakfast
 
  
• Session 1 - Signs, symptoms and laboratory findings from a health care perspective: The need for ontology
+
'''Day 2: Thursday, September 4''' (Room: Irving I-III, Lobby Level)
  
:: David Karp (Dallas)? - Combining clinical exam and laboratory findings in the rheumatology clinic
+
8:30am - Continental Breakfast
:: 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
+
9:00am - Session 4: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms (Lewis, moderator)
  
• Session 2 - Standardization of clinical and laboratory data in the context of clinical and translational research - use cases, strategies and vision
+
::: Laboratory data and metadata in laboratory information systems [http://ontology.buffalo.edu/08/phenotype/BURGUN.ppt slides] (Anita Burgun)
 +
::: An ontology-based approach for connecting disease pathogenesis with clinical/laboratory data [http://ontology.buffalo.edu/08/phenotype/SCHEUERMANN.ppt slides] (Richard Scheuermann)
  
:: Chris Chute (Rochester, MN)? - Data standards from patient care to clinical and translational research - the CTSA perspective
+
10:30am - Refreshment Break
:: 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'''
+
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 [http://ontology.buffalo.edu/08/phenotype/LEWIS.ppt slides] (Suzanna Lewis)
  
8:30am Continental Breakfast
+
12:00pm - Lunch Break
  
Session 3 - Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms
+
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)
  
::      William Hogan (Pittsburgh) - Problems with current approaches to clinical data
+
2:30pm - Refreshment Break
:: 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
+
2:45pm - Session 6 (continued)
  
12:00 Lunch
+
4:00pm - Close
  
• 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.
+
==Summary of Workshop==
  
4:00pm Close
+
* Summary [http://esw.w3.org/topic/HCLSIG/Meetings/2008-10-02_Conference_Call?action=AttachFile&do=get&target=NCBO_clinical_phenotype_ont.pdf slides] (Kei Cheung)
  
==Provisional List of Participants==
+
==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.
+
[[image:photo.jpg|thumb|right]]
  
('''**''' = Registration form received)
+
*Jonas Silva Almeida (MD Anderson Cancer Center / University of Texas)
*Jonas Silva Almeida (University of Texas MD Anderson Cancer Center)'''**'''
+
*Sivaram Arabandi (Heart & Vascular Institute / Cleveland Clinic)
*Sivaram Arabandi (Cleveland Clinic Semantic Database for Cardiovascular Surgery)'''**'''
+
*John M. Armstrong (Lead Horse Technologies, Inc.)
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)'''**'''
+
*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)
*Elmer V. Bernstam (University of Texas Health Science Center at Houston)'''**'''
+
*Bruce Bray (Dept of Biomedical Informatics, University of Utah)
*Olivier Bodenreider (Medical Ontology Research, National Library of Medicine / NIH)'''**'''
+
*Anita Burgun (Université de Rennes)
*Anita Burgun (Université de Rennes)'''**'''
+
*Kei-Hoi Cheung (Senselab / Yale Center for Medical Informatics)
*Helen Chen (Phillips)
+
*Christopher G. Chute (National Center for Biomedical Ontology / Mayo Clinic)
*Kei Cheung (Senselab / Yale University)
+
*Paolo Ciccarese (Mass General Hospital / Harvard Medical School)
*Christopher Chute (NCBO / Mayo Clinic)'''**'''
+
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)
*Timothy W. Clark (Mass General Institute for Neurodegenerative Disease / Harvard Medical School)'''**'''
+
*Gianluca Colombo (University of Milano-Bicocca, DISCo)
*Gianluca Colombo (University of Milano-Bicocca, DISCo)'''**'''
+
*Tommie G. Curtis (SAIC, NCICB Contractor)
*Amar K. Das (Stanford Center for Biomedical Informatics Research)
+
*Amar K. Das (Center for Biomedical Informatics Research / Stanford University)
*Louis J. Goldberg (Ontology Research Group / University at Buffalo)'''**'''
+
*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)
*Herb Hagler (University of Texas Southwestern Medical Center at Dallas)'''**'''
+
*William Hogan (University of Pittsburgh Medical Center)
*Carol Hamilton (RTI International)
+
*Zhang-Zhi Hu (PRO / Georgetown University Medical Center)
*William Hogan (University of Pittsburgh Medical Center)'''**'''
+
*Charles Jaffe (Health Level 7, Inc. (HL7))
*Zhang-zhi Hu (PRO / Georgetown University Medical Center)'''**'''
+
*Andrew G. James (Division of Neonatology, The Hospital for Sick Children / University of Toronto)
*Charles Jaffe (HL7)
+
*David Karp (University of Texas Southwestern Medical Center at Dallas)
*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)
 
*Bron Kisler (CDISC)
 +
*Megan Kong (University of Texas Southwestern Medical Center at Dallas)
 
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
 
*Suzanna Lewis (Lawrence Berkeley National Laboratory)
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)'''**'''
+
*Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)
*Meredith L. Nahm (Duke Translational Medicine Institute)'''**'''
+
*Pradeep Mutalik (Yale Center for Medical Informatics)
*Chimezie Ogbuji (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
+
*Chimezie Ogbuji (Cleveland Clinic Foundation)
*Christopher Pierce (Heart and Vascular Institute / Cleveland Clinic)'''**'''
+
*John Quinn (Health Level 7, Inc. (HL7))
*John Quinn (HL7)
+
*Alan Ruttenberg (Science Commons / Neurocommons)
*Dianne M. Reeves (NCI CBIIT / NIH)
+
*Neil Sarkar (Marine Biological Laboratory)
*Alan Ruttenberg (Science Commons / Neurocommons)'''**'''
 
*Neil Sarkar (Marine Biological Laboratory, Woods Hole)'''**'''
 
 
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
 
*Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)'''**'''
+
*Lynn M. Schriml (Institute for Genome Sciences, University of Maryland)
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)'''**'''
+
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)
*Kent A. Spackman (International Health Terminology Standards Development Organization)'''**'''
+
*Kent A. Spackman (International Health Terminology Standards Development Organization)
*Samson Tu (Stanford Center for Biomedical Informatics Research)
+
*Larry Streepy (Cleveland Clinic Foundation)
*Ashley Xia (NIAID / NIH)'''**'''
+
*Gary Walker (Quintiles)
*W. Jim Zheng (Biomedical Ontology Research Group, Medical University of South Carolina)'''**'''
+
*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.
+
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==
 
==Suggested Background Reading==
 +
 +
[http://ontology.buffalo.edu/medo/continua.pdf Continua in Biological Systems], Stefan Schulz and Ingvar Johansson, The Monist, 2007; 90(4), 499-522.
  
 
[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration
 
[http://nuke.neurowebkc.eu/LinkClick.aspx?fileticket=opFTkenwCz0%3D&tabid=66&mid=435 NEUROWEB Project]: From Clinically-Based Phenotypes to Genomics Integration
Line 140: Line 180:
  
 
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1781118 PhenomicDB]: A New Cross-Species Genotype/Phenotype Resource
 
[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, The Monist, 2007; 90(4): 555-584.
 +
 +
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1948102 Human disease classification in the postgenomic era], J. Loscalzo, I. Kohane and A.-L. Barabasi
  
 
==Useful Links==
 
==Useful Links==
Line 150: Line 198:
  
 
[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]
 
[http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotypic Quality Ontology]
 +
 +
==Proposed Terms and Definitions==
 +
 +
* [[Clinical Phenotypes | Toward an Ontological Treatment of the Initiation, Realization, Recognition, and Representation of Disease]]
 +
 +
==Follow-Up Meeting 2009==
 +
 +
[http://bimib.disco.unimib.it/index.php/SSFW09 Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes]

Latest revision as of 07:44, 7 April 2009

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

Workshop organized by:

Richard Scheuermann, University of Texas Southwestern Medical Center, Dallas

Barry Smith, National Center for Biomedical Ontology / University at Buffalo


Sponsored by:

University of Texas Southwestern Medical Center Clinical and Translational Science Award (CTSA) Program

National Center for Biomedical Ontology (NCBO)

Lead Horse Technologies, Inc.


Date:

September 3-4, 2008


Venue:

Dallas/Fort Worth Airport Marriott [1].

  • 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: [2].

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 in 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 I-III, Lobby Level)

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 slides (David Karp)
Clinical signs and findings in neonatology slides (Andrew James)

10:30am - Refreshment Break

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

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

12:00pm - Buffet Lunch (Arlington Room, Lower Level), Provided by the generous support of Lead Horse Technologies, Inc.

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

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

3:00pm - Refreshment Break

3:30pm - Session 3 continued (Ruttenberg, moderator)

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

5:30pm - Reception (Grand Prairie Room, Lower Level), Provided by the generous support of The Cleveland Clinic Foundation SemanticDB


Day 2: Thursday, September 4 (Room: Irving I-III, Lobby Level)

8:30am - Continental Breakfast

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

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

Summary of Workshop

Participants

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  • 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)
  • 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)
  • Megan Kong (University of Texas Southwestern Medical Center at Dallas)
  • Suzanna Lewis (Lawrence Berkeley National Laboratory)
  • Daniele Merico (NEUROWEB / University of Toronto & University of Milano-Bicocca, DISCo)
  • Pradeep Mutalik (Yale Center for Medical Informatics)
  • Chimezie Ogbuji (Cleveland Clinic Foundation)
  • 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)
  • Gary Walker (Quintiles)
  • 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

Continua in Biological Systems, Stefan Schulz and Ingvar Johansson, The Monist, 2007; 90(4), 499-522.

NEUROWEB Project: From Clinically-Based Phenotypes to Genomics Integration

OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

Ontology-Guided Data Preparation for Discovering Genotype-Phenotype Relationships

PhenomicDB: A New Cross-Species Genotype/Phenotype Resource

What is a Diagnosis?, Werner Ceusters

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.

The Factory Model of Disease, Neil Williams, The Monist, 2007; 90(4): 555-584.

Human disease classification in the postgenomic era, J. Loscalzo, I. Kohane and A.-L. Barabasi

Useful Links

Mammalian Phenotype Ontology

NCBO Bioportal

OBO Foundry

Phenotypic Quality Ontology

Proposed Terms and Definitions

Follow-Up Meeting 2009

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes