Anatomy Ontology Workshop

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 its relation to species specific anatomies
• Relations and development in CARO
• The top level CARO universals
• Concrete steps to implement CARO

Participation

PLEASE NOTE THAT PARTICIPATION IS RESTRICTED. For the usual practical reasons we need 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

Louis Goldberg -– Oral Biology, University at Buffalo

Melissa Haendel -– Zebrafish Information Network, University of Oregon

Marc Halfon -– Biochemistry, University at Buffalo

Terry Hayamizu -– The Jackson Laboratory

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 in Seattle, WA. Registration and accommodation details will be provided to participants in due course.