Workshop on Ontology of Diseases

General Information

The National Center for Biomedical Ontology hosted a two-day workshop focused on the ontology of disease on November 6-7, 2006 in Baltimore, MD.

Goals

The goals of this workshop are:

1. to determine the principal purposes to which ontologies can be put in the annotation and processing of disease-related data and information
2. to introduce biologists, bioinformaticians, clinical researchers and other interested persons to the theories, tools and methods of ontology
3. to address fundamental issues pertaining to the nature of disease
4. to create a consensus-based strategy for the most effective and useful realization of these purposes
5. to foster cooperation between people who work in this and related fields.

To realize these goals we shall seek to achieve clarity on the following questions:

1. What is the correct definition of disease?
2. What are the different kinds of entities that will need to be recognized in a disease ontology?
3. What are the relations between disease and diagnoses, findings, signs and symptoms?
4. What are the relations between disease types and disease instances?
5. What are the relations between disease and the anatomical entities and biological processes at different (molecular, cellular, physiological) levels of granularity and at different stages in the course or history of a given disease instance?
6. What is the relation between pathological independent continuants like carcinomas and dependent continuants such as the cancer disease itself?
7. How are we to understand the relation between a virus and the condition of being infected with a virus?
8. What classificatory principles (‘axes’) should be employed in the construction of a disease ontology:
   • organized by anatomic entity
   • organized by biological process
   • organized by biological function
   • organized by clinical and pre-clinical manifestation
   • organized by etiological agent like virus or chemical (using appropriate external ontologies)?
9. What are the appropriate relations between the different kinds of entities?
   • within the disease ontology itself, and
   • between the disease ontology and other ontologies, such as an anatomical ontology (e.g. the FMA)?
10. How is the disease ontology related to neighboring ontologies such as PATO and the Gene Ontology Biological Process ontology?
11. What is the relationship between human diseases and their animal models?

Agenda

Monday November 6

Morning

• 8.30am Registration and Continental Breakfast
• 9am Participant Self-Introductions

Session I: Disease Ontologies - Where We Are (Moderator: Rex Chisholm) Audio

• 9.15am Kent Spackman: SNOMED CT Slides
• 10.15am Minna Lehvaslaiho: eVOC Ontologies
• 11.15am Coffee
• 11.30am Rex Chisholm: OBO Disease Ontology

Afternoon

• 12.45pm Lunch Break

Session II: What is a Disease? (Moderator: Barry Smith) Audio

• 2.00pm What a Disease Ontology is For: Slides
• 3.00pm Neil Williams: The Ontology of Powers, Dispositions and Tendencies: Slides
• 3.30pm Coffee
• 4.00pm How to Build a Disease Ontology

Tuesday November 7

Morning

• 8.30am Continental Breakfast

Session III: Disease and Diagnosis (Moderator: Werner Ceusters)

• 9am Louis J. Goldberg: Networks and the Ontology of Disease Slides Audio
• 10.30am Coffee
• 11am Werner Ceusters: The Ontology of Diagnosis: Slides Audio

Afternoon

• 12.45pm Lunch Break

Session IV: The Next Steps: Moderated Discussion (Moderatrix: Suzanna Lewis) Audio

• 2.00pm Chris Mungall: DO and the OBO Foundry [Slides
• 2.30pm Owen White: Pragmatic Steps Forward
• 3.30pm Coffee
• 4.00pm Strategy Session

Participants

Carol Bean -– National Center for Research Resources, National Institutes of Health, U.S.A

Olivier Bodenreider -– National Library of Medicine, U.S.A

Werner Ceusters -– ECOR, Saarland University, Germany

Rex L. Chisholm -– Center for Genetic Medicine, Northwestern University, U.S.A

Christopher G. Chute -– NCBO, Mayo Clinic College of Medicine, U.S.A

Elaine Collier -– National Center for Research Resources, National Institutes of Health, U.S.A

Lindsay G. Cowell -– Center for Computational Immunology, Duke University, U.S.A

Janan T. Eppig -– The Jackson Laboratory, U.S.A

Yong Gao -– Massachusetts General Hospital, Harvard Medical School, U.S.A

Louis J. Goldberg -– Oral Biology, University at Buffalo, U.S.A

Peter Good -– National Human Genome Research Institute, U.S.A

Jeffrey S. Grethe -- BIRN, University of California at San Diego, U.S.A

Kristel Hackett -– MGH Laboratory of Computer Science, U.S.A

Frank Hartel -– National Cancer Institute, National Institutes of Health, U.S.A

Beth Huffer -- Ontology Works, Baltimore MD, U.S.A.

Waclaw Kusnierczyk -- Norwegian University of Science and Technology, Trondheim

Dirk Lanzerath -– German Reference Centre for Ethics in the Life Sciences, Germany

Minna Lehvaslaiho -- SANBI, University of the Western Cape, South Africa

Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory, U.S.A

Jose (Onard) Mejino -– Structural Informatics Group, University of Washington, U.S.A

Chris Mungall -– NCBO, Lawrence Berkeley National Laboratory, U.S.A

Fabian Neuhaus -– NCBO, University at Buffalo, U.S.A

Alan L. Rector -- Computer Science, University of Manchester, U.K.

Richard H. Scheuermann -– Pathology, U.T. Southwestern Medical Center, U.S.A

Lynn Schriml -- The Institute for Genomic Research, Rockville MD, U.S.A.

Stefan Schulz -– Medical Informatics, Freiburg University Hospital, Germany

Kent A. Spackman -– Medical Informatics, Oregon Health & Science University, U.S.A

Barry Smith -– NCBO, University at Buffalo, U.S.A

Lowell Vizenor -- Ontology Works, Baltimore MD, U.S.A.

Nicole Washington -- NCBO, Lawrence Berkeley National Labs., Berkeley CA, U.S.A.

Monte Westerfield -– Institute of Neuroscience, University of Oregon, U.S.A

Owen White -– The Institute for Genomic Research, Rockville MD, U.S.A

Neil Williams -– Philosophy, University at Buffalo, U.S.A

Venue

Inn at the Colonnade

4 West University Parkway

Baltimore, Maryland 21218

Telephone: +1 410 235 5400

Fax: +1 410 235 5572

The Inn at the Colonnade is located across from Johns Hopkins University, less than four miles from Baltimore's CBD and historic Inner Harbor, and only 20 minutes from BWI International Airport.

A block of rooms has been reserved for those Workshop participants and attendees wishing to stay at the Inn at the Colonnade. Reservations may be made by calling 1-800-222-TREE. When making reservations, workshop participants and attendees are asked to identify themselves as being a member of the NCBO group. All reservations must be guaranteed for late arrival by charging to a major credit card. Workshop participants and attendees are encouraged to make room reservations no later than 10/15/06. After 10/15/06, the Inn at the Colonnade may offer unused rooms held in the NCBO block to other customers. Reservations requested by Workshop participants and attendees after 10/15/06 will be accepted by the Inn at the Colonnade based upon availability and prevailing rates.

Definitions of Disease

Proposed WHO definition of disease (with thanks to Bedirhan Ustun):

• A disease is:
• an interconnected set of one or more dysfunctions in one or more body systems including:
  • a pattern of signs, symptoms and findings (symptomatology - manifestations)
  • a pattern or patterns of development over time (course and outcome)
  • a common underlying causal mechanism (etiology)
• linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
• and possibly: to a pattern or patterns of response to interventions (treatment response)

Definition from Christopher Boorse:

• A disease is:
• a type of internal state which is either an impairment of normal functional ability--that is, a reduction of one or more functional abilities below typical efficiency--or a limitation on functional ability caused by environmental agents.

From: What Is Disease? J. M. Humber, R. F. Almeder, Eds., Humana Press, Totowa, NJ, 1997.

Definition from Lawrie Reznek's Abnormality Theory:

• A disease is:

• a state of a person which issues in abnormal behavior.

• Something is an abnormal bodily or mental process if it does standard members of the human species some harm in standard circumstances

• Something does a person harm if it makes the person less able to live a good or worthwhile life.

Definition from Larissa et al., "Defining Disease in the Genomics Era"

• A disease is:
• a state that places individuals at increased risk of adverse consequences.
• Treatment is given to those with a disease to prevent or ameliorate adverse consequences.
• The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease.

Definitions from Smith et al.:

• An anatomical structure is pathological whenever:
  • it has come into being as a result of changes in some pre-existing canonical anatomical structure
  • through processes other than the expression of the normal complement of genes of an organism of the given type, and
  • is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.

• An organism (or part of an organism) is diseased if and only if
  • it includes among its parts pathological anatomical structures which
  • compromise the organism’s physiological processes to the degree that they give rise to symptoms and signs.

Definitions from UMLS Metathesaurus:

MeSH A disease is: A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown.

CRISP Thesaurus: top term heading for all specific disorders and diseases; a disease is a deviation from or interruption of the normal structure or function of any part, organ or system (or combination thereof) of the body that is manifested by a characteristic set of symptoms and signs; a disorder is a derangement or abnormality of function.

Psychological Index Terms: Conceptually broad term referring primarily to physical illness. Also used when particular disorders are not specified. Use a more specific term if possible. For general discussions of health impairment consider also the term HEALTH.

NCI Thesaurus: A disease is: any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. Sometimes the term is used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.

Encyclopedia Britannica: Disease is "a harmful deviation form the normal structural or functional state of an organsim."

Links

The workshop is associated with FOIS 2006 and KRMed 2006.

Biohealthbase

OBO Disease Ontology

The OBO Foundry

eVOC Ontologies

Physiome Project

SNOMED

Some papers on SNOMED.

Literature

Anita Burgun, Olivier Bodenreider, Christian Jacquelinet Issues in the Classification of Disease Instances with Ontologies, MIE 2006.

Amarnath Gupta et alia: Towards a formalization of disease-specific ontologies for neuroinformatics.

Cornelius Rosse, Anand Kumar, Jose LV Mejino Jr, Daniel L Cook, Landon T Detwilern and Barry Smith, A Strategy for Improving and Integrating Biomedical Ontologies

Barry Smith, Werner Ceusters, Anand Kumar and Cornelius Rosse, On Carcinomas and Other Pathological Entities, Comparative and Functional Genomics

Neil Williams, The Factory Model of Disease, The Monist, October 2007, Volume 90, Number 4.