Anatomy Ontology Workshop

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General Information

The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. The workshop will take place on September 8-9, 2006 in Seattle.

Aim of the workshop

At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy ontologies for a variety of organisms. Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species.

The main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies.

Its objectives are to develop:

1. a list of relations (especially part_of) used within anatomical anatomies, including definitions and rules for consistent use within anatomy ontologies ;

2. a list of major organizational units of biological organisms at all levels of granular partitions (e.g. biological macromolecule, cell, organ);

3. a representation of developmental stages of organisms; are anatomy and development two separate or one single integrated ontology? If separate what are the relations between them and how should they be applied;

4. a method that allows automated reasoners to recognize homologous anatomical structures of different species.

Agenda

In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. This common ontology will comprehend both top-level categories and a common set of relations to be used within anatomical ontologies; CARO will be embedded in a  set of principles for constructing anatomy ontologies for different organisms at different developmental stages. The discussion will be based on a pre-version of CARO.

The workshop will consist of four sessions (not necessarily in this order):

  • The Range of CARO and it's Relation to Species Specific Anatomies
  • Relations and Development in CARO
  • The Top Level CARO Universals
  • Concrete Steps to Implement CARO

Participation

For the usual practical reasons we want to keep the number of people attending small. This workshop is not open for participants who have only passing interest; we want to limit it to those who are in the trenches building these ontologies, since it sharpens the mind to have a tangible problem to be solved. Requests for participation are welcome. Please send a brief statement of your expertise to Fabian Neuhaus.

Participants

Michael Ashburner -– NCBO, University of Cambridge

Carol Bean -– National Institutes of Health

Albert Burger -– Medical Research Council, Human Genetics Unit, Edinburgh

Sherri De Coronado -– National Cancer Institute, Center for Bioinformatics

Melissa Haendel -– Zebrafish Information Network, University of Oregon

Thorsten Henrich -– European Molecular Biology Laboratory

Ira Kalet -– Radiation Oncology, Biomedical Informatics, University of Washington

Jennifer Leopold -– Computer Science, University of Missouri-Rolla

Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory

Paula Mabee -– Biology, University of South Dakota

Anne Maglia -– Biological Sciences, University of Missouri-Rolla

Onard Mejino -– Structural Informatics Group, University of Washington

Chris Mungall -– NCBO, Lawrence Berkeley National Laboratory

Fabian Neuhaus -– NCBO, University at Buffalo

Alan Rector -– Medical Informatics, University of Manchester

Martin Ringwald -– The Jackson Laboratory

Cornelius Rosse -– Structural Informatics Group, University of Washington

Indra Neil Sarkar -– Invertebrate Zoology, American Museum of Natural History

Nigam Shah -– NCBO, Stanford Medical Informatics

Barry Smith -– NCBO, University at Buffalo

Ravensara Travillian -– Structural Informatics Group, University of Washington

Monte Westerfield -– Institute of Neuroscience, University of Oregon

Venue

The event will be held at:

Silver Cloud Inns / Seattle-University Village

5036 25th Avenue NE

Seattle, WA 98105

Phone: 206-526-5200


Silver Cloud Inns / Seattle-University Village is located just one mile from the University of Washington main campus, and two blocks from the upscale University Village shopping center. A complimentary continental breakfast is offered daily (6:30-9:30am M-F, 7:00-10:00am Sat/Sun). A fitness center, year round indoor pool and spa, and local area shuttle service is also available to Silver Cloud Inn guests.

All guest rooms have complimentary high-speed internet access, microwaves, and refrigerators. We have negotiated a special guest room rate for Workshop attendees of $119 per night for a Standard King or Double Queen guest room. (For those Workshop participants wishing to extend their stay in Seattle, this rate will be offered for 3 days prior and/or after the conclusion of the event.) In order to receive this special rate, WORKSHOP PARTICIPANTS MUST MAKE ROOM RESERVATIONS BY AUGUST 24, 2006. After this date, all unreserved rooms within the NCBO block will be released for general sale at prevailing rates.


To make room reservations online:

1. Visit www.silvercloud.com

2. Select "Reservations"

3. Select "Seattle-University District" under Properties

4. Select "Group"

5. Type in "Group Number": NCBO

6. Type in "Password": NCBO

7. Complete reservation


To make room reservations via telephone:

1. Call the hotel directly at 206-526-5200 or 800-205-6940

2. Be sure to indicate that you are with the "NCBO Workshop" group (Group code: NCBO).