Anatomy Ontology Workshop

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Contents

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. Preliminary discussions are posted here. Listserv archives are available here.

Participation

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

Agenda and Links to Meeting Minutes and Powerpoint Presentations

Minutes and Powerpoints posted on Shared_Materials#CARO_September_2006_meeting

Friday

  • 9: 30am Session I: Principles of Ontology Design (Smith, Mungall)
  • 2.00pm Session II: Current state of model organism anatomy ontologies (Haendel, Osumi-Sutherland)
  • Saturday
  • 9.00am Session III: CARO a common anatomy reference ontology (Rosse)
  • 2pm Session IV: Intelligent grouping of curations and use cases (Haendel, Osumi-Sutherland)
  • 4pm Session V: Future Steps (Smith)

Participants

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

Venue

The event will be held in Seattle, WA.


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