Anatomy Ontology Workshop
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. Preliminary discussions are posted here. Listserv archives are available here.
PLEASE NOTE THAT REGISTRATION IS CLOSED.
If you have any suggestions or questions about the workshop, please don't hesitate to contact Fabian Neuhaus.
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.
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.
Issues to be addressed include:
- 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
Please also see the CARO wiki for discussion notes and other information. http://www.bioontology.org/wiki/index.php/CARO:Main_Page
Friday 9:00am Participant self-introductions 9: 30am Session I: Principles of Ontology Design (Smith, Mungall) 10:30am Coffee 11:00am Session I (continued) 12:30pm Lunch 2.00pm Session II: Current state of model organism anatomy ontologies (Haendel, Osumi-Sutherland) 3:30pm Coffee 4:00pm Session II (continued)
Saturday 9.00am Session III: CARO a common anatomy reference ontology (Cook, Mejino, Rosse) 10:30am Coffee 11:00am Session III (continued) 12:30pm Lunch 2pm Session IV: Intelligent grouping of curations and use cases (Haendel, Osumi-Sutherland) 3:30pm Coffee 4pm Session V: Future Steps (Smith)
Stuart Aitken -– Artificial Intelligence Applications Institute, University of Edinburgh
Michael Ashburner -– NCBO, University of Cambridge
Thomas Bittner -– Philosopy, University at Buffalo
Judith Blake -– The Jackson Laboratory
Albert Burger -– Medical Research Council, Human Genetics Unit, Edinburgh
Rex Chisholm -– Center for Genetic Medicine, Northwestern University
Sherri De Coronado -– National Cancer Institute, Center for Bioinformatics
Louis Goldberg -– Oral Biology, University at Buffalo
Peter Good -– National Human Genome Research Institute
Melissa Haendel -– Zebrafish Information Network, University of Oregon
Marc Halfon -– Biochemistry, University at Buffalo
Terry Hayamizu -– The Jackson Laboratory
David Hill -– The Jackson Laboratory
Ira Kalet -– Radiation Oncology, Biomedical Informatics, University of Washington
Raymond Lee -– Biology, California Institute of Technology
Jennifer Leopold -– Computer Science, University of Missouri-Rolla
Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory
Kitsos Louis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas
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
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
David Osumi-Sutherland -– Genetics, University of Cambridge
Pantelis Topalis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas
Ravensara Travillian -– Structural Informatics Group, University of Washington
Peter Vize -– Biology, University of Calgary
Monte Westerfield -– Institute of Neuroscience, University of Oregon
The event will be held in Seattle, WA.