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
+
[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://biontology.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.
 
:There is no participation fee, and refreshments will be provided through the course of the meeting.
 
  
This meeting is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028, the Clinical and Translational Science Award (1 U54 RR023468) and the Bioinformatics Integration Support Contract (1 N01 AI40076).  
+
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].
 
Information on the National Centers for Biomedical Computing can be found at: [http://nihroadmap.nih.gov/bioinformatics].
Line 24: Line 38:
 
==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)
 +
 
 +
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.''''']
 +
 
 +
1:00pm - Session 3: Standardization of clinical and laboratory data in the context of clinical and translational research (Jaffe, moderator)
  
*Utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory findings, and their interrelations.
+
::: 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)
  
*Delineate the roles that signs, symptoms and findings play in both clinical patient management and in clinical research.
+
3:00pm - Refreshment Break
  
*Develop a clear understanding and representation of the distinction between clinical and pre-clinical manifestations of signs, symptoms and findings.
+
3:30pm - Session 3 continued (Ruttenberg, moderator)
  
*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
+
::: 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)
  
*Explore incorporation of the results of this work into the CTSA Human Studies Metadata Repository framework
+
5:30pm - Reception (Grand Prairie Room, Lower Level), '''''Provided by the generous support of The Cleveland Clinic Foundation SemanticDB'''''
  
==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. The following is a provisional list of attendees:
+
'''Day 2: Thursday, September 4''' (Room: Irving I-III, Lobby Level)
  
*Jonas Silva Almeida (University of Texas MD Anderson Cancer Center)
+
8:30am - Continental Breakfast
*Sivaram Arabandi (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
 
*Robert Arp (National Center for Biomedical Ontology / University at Buffalo)
 
*Elmer V. Bernstam (University of Texas at Houston)
 
*Bron Kisler (CDISC)
 
*Anita Burgun (Université de Rennes)
 
*Helen Chen (Phillips)
 
*Kei Cheung (Senselab / Yale University)
 
*Chris Chute (Mayo Clinic)
 
*Tim Clark (Harvard)
 
*Sherri de Coronado (National Cancer Institute / NIH)
 
*Amar K. Das (Stanford Center for Biomedical Informatics Research)
 
*Louis J. Goldberg (University at Buffalo)
 
*Jeffrey S. Grethe (BIRN / University of California at San Diego)
 
*Herb Hagler (University of Texas Southwestern Medical Center)
 
*Udo Hahn (University of Jena)
 
*William Hogan (University of Pittsburgh Medical Center)
 
*Zhangzhi Hu (PRO / Georgetown University)
 
*Charles Jaffe (HL7)
 
*Andrew James (Division of Neonatology, The Hospital for Sick Children, Toronto)
 
*David Karp (University of Texas Southwestern Medical Center)
 
*Suzanne Lewis (Lawrence Berkeley National Laboratory)
 
*Daniele Merico (NEUROWEB)
 
*Meredith Nahm (Duke Translational Medicine Institute)
 
*Chimezie Ogbuji (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
 
*Chris Pierce (Cleveland Clinic Semantic Database for Cardiovascular Surgery)
 
*John Quinn (HL7)
 
*Dianne M. Reeves (NCI CBIIT / NIH)
 
*Daniel Rubin (Stanford Center for Biomedical Informatics Research)
 
*Alan Ruttenberg (Science Commons / Neurocommons)
 
*Neil Sarkar (Marine Biological Laboratory, Woods Hole)
 
*Richard Scheuermann (University of Texas Southwestern Medical Center)
 
*Lynn Schriml (University of Maryland)
 
*Barry Smith (National Center for Biomedical Ontology / University at Buffalo)
 
*Kent 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.
+
9:00am - Session 4: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms (Lewis, moderator)
  
==Tentative Agenda==
+
::: 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)
  
'''Day 1: Wednesday, September 3'''
+
10:30am - Refreshment Break
  
8:30am Registration and Continental Breakfast
+
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)
  
• Session 1 - Health care and clinical research perspective
+
12:00pm - Lunch Break
:: Presentations by local clinicians and clinical investigators
 
:: Presentations of selected CTSA use cases
 
  
Session 2 - Brief overview of ontology formalisms
+
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)
  
• Session 3 - Brief presentations of existing and emerging standards regarding the use of terminologies related to signs, symptoms and findings
+
2:30pm - Refreshment Break
  
Session 4 - Proposals for ontology-based clarification and unification of ‘sign’, ‘symptom’, ‘finding’ and related terms with the goal of achieving improved understanding of what they are and how they relate to each other
+
2:45pm - Session 6 (continued)
  
'''Day 2: Thursday, September 4'''
+
4:00pm - Close
  
8:30am Continental Breakfast
+
==Summary of Workshop==
  
• Session 5 - Working session to utilize consistent ontological design and development principles to describe disease signs and symptoms, clinical and laboratory finding, and their interrelations
+
* 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)
  
• Session 6 - 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
+
==Participants==
  
4:00pm Close
+
[[image:photo.jpg|thumb|right]]
 +
 
 +
*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==
 
==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 126: 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 133: Line 195:
 
[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]
 
[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]
  
OBO Foundry [http://obofoundry.org ontologies]
+
[http://obofoundry.org OBO Foundry]
  
 
[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