DallasWorkshop

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)

Date:

September 3-4, 2008

Venue:

Dallas/Fort Worth Airport Marriott [1].

• To take advantage of discounted rate at the 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 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

8:30am - Registration and Continental Breakfast

9:00am - Opening remarks

Richard Scheuermann (Dallas) - Workshop goals

9:15am - 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

10:30am - Refreshment Break

10:45am - Session 1 (continued)

Sivaram Arabandi (Cleveland) - Reasoning with clinical exam and laboratory findings: The Cleveland experience

12:00pm - Lunch Break

1:00pm - Session 2: Standardization of clinical and laboratory data in the context of clinical and translational research - use cases, strategies and vision

Suzanne Lewis (LNL, Berkeley) - PATO and Phenote: From model organism phenotypes to clinical medicine

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

3:00pm - Refreshment Break

3:30pm - Session 2 (continued)

Kent Spackman (IHTSDO, Portland) - The future of SNOMED-CT in the representation of clinical findings

William Hogan (Pittsburgh) - Problems with current approaches to clinical data

Day 2: Thursday, September 4

8:30am - Continental Breakfast

9:00am - Session 3: Proposals for unification of standard terminologies for the representation ‘sign’, ‘symptom’, ‘finding’ and related terms

Olivier Bodenreider (Bethesda) 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

10:30am - Refreshment Break

10:45am - Session 4: Working session to explore how consistent ontological design and development principles can lead to enhanced representation of signs and symptoms, clinical and laboratory finding, and their interrelations

12:00pm - Lunch Break

1:00pm - 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 biology and bioinformatics communities.

2:30pm - Refreshment Break

2:45pm - Session 5 (continued)

4:00pm - Close

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 [3] as soon as possible.

(** = Confirmed Registrant)

• Jonas Silva Almeida (MD Anderson Cancer Center / University of Texas)**
• Sivaram Arabandi (Heart & Vascular Institute / Cleveland Clinic)**
• 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)**
• Bruce Bray (Dept of Biomedical Informatics, University of Utah)**
• Anita Burgun (Université de Rennes)**
• Helen Chen (Phillips)
• 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)**
• 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)**
• 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 (HL7)
• 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

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

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

Mammalian Phenotype Ontology

NCBO Bioportal

OBO Foundry

Phenotypic Quality Ontology