Difference between revisions of "Workshop on Ontology of Diseases"
| Line 178: | Line 178: | ||
**is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. | **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 | + | *An organism (or part of an organism) is '''diseased''' if and only if |
**it includes among its parts pathological anatomical structures which | **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. | **compromise the organism’s physiological processes to the degree that they give rise to symptoms and signs. | ||
Revision as of 07:54, 17 October 2006
General Information
The National Center for Biomedical Ontology will host a two-day workshop focused on the ontology of diseases on November 6-7, 2006 in Baltimore, MD.
The goals of the workshop are to promote sound, principles-based ontology construction and to raise the level of cooperation between people who work in this and related fields.
Please note that registration is closed. If you have any suggestions or questions about the workshop, please contact Fabian Neuhaus.
Goals
The goals of this workshop are:
- 1. to introduce biologists, bioinformaticians, clinical researchers and other interested persons to the theories, tools and methods of ontology;
- 2. to address fundamental issues pertaining to the nature of disease;
- 3. to determine the principal purposes to which ontologies can be put in the annotation and processing of disease-related data and information and to create an ontology-focused strategy for the most effective and useful realization of these purposes
- To realize these goals we shall seek to achieve clarity as concerns the following questions:
- i. what is the correct definition of disease?
- ii. how are diseases related (a) to diagnoses, findings, signs and symptoms, and (b) to anatomical entities and biological processes at different (molecular, cellular, physiological) levels of granularity?
- iii. what classificatory principles (‘axes’) should be employed in the construction of a disease ontology?
- iv. how is the disease ontology related to neighboring ontologies such as PATO and the Gene Ontology Biological Process ontology?
- v. what relations should be employed (a) within the disease ontology itself, and (b) between the disease ontology and other ontologies such as the FMA
Agenda
Monday November 6
Morning
- 8.30am Registration and Continental Breakfast
- 9am Participant Introductions
Session I: Disease Ontologies - Where We Are (Moderator: Rex Chisholm)
- 9.15am Rex Chisholm: OBO Disease Ontology
- 10.15am Coffee
- 10.30am Minna Lehvaslaiho: eVOC Ontologies
- 11.30am Coffee
- 11.45am Kent Spackman: SNOMED CT
Afternoon
- 1.00pm Lunch
Session II: What is a Disease? (Moderator: Barry Smith)
- 2.00pm What a Disease Ontology is For
- 3.00pm Neil Williams: The Ontology of Powers, Dispositions and Tendencies
- 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
- 10.30am Coffee
- 11am Werner Ceusters: The Ontology of Diagnosis
Afternoon
- 1pm Lunch
Session IV: The Next Steps: Moderated Discussion (Moderatrix: Suzanna Lewis)
- 2.00pm Chris Mungall: DO and the OBO Foundry
- 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 -- University of San Diego
Kristel Hackett -– MGH Laboratory of Computer Science, U.S.A
Frank Hartel -– National Cancer Institute, National Institutes of Health, U.S.A
Ingvar Johansson -– IFOMIS, Saarland University, Germany
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
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 have 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)
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.
Links and Literature
The workshop is associated with FOIS 2006 and KRMed 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
Some papers on SNOMED.