Ontology and Cellular Networks

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General Information

The National Center for Biomedical Ontology will host a two-day workshop focused on ontology and cellular networks on October 30-31, 2007 in Newark, NJ. The meeting will be organized jointly with the MagNet Center for Multiscale Analysis of Genetic and Cellular Networks.


The goals of this workshop are:

  • 1. to bring together those in the various NCBCs and in related organizations with an interest in ontology
  • 2. to provide an introduction to the basic tools and methods of ontology
  • 3. to advance the work of the Scientific Ontology SWIG
  • 4. to initiate discussion on developing an ontology of cellular networks.


Tuesday October 30


  • 8.30am Registration and Continental Breakfast
  • 9am Participant Self-Introductions

Session I: Overview of NCBC Collaborative Work in Ontology

  • Moderator: Peter Lyster (NIH/NIGMS)
  • 9.15am David States (NAMIC)
  • 10.00am Chris Mungall (NCBO)
  • 11.15am Coffee
  • 11.30am Representatives from other NCBCs


  • 12.45pm Lunch Break

Session II: Ontologies for Cellular Networks (Part 1)

  • 2.00pm Barry Smith (NCBO): A Vision for the Future of Biomedical Ontology
  • 2.45pm Lindsay Cowell (Duke): The Cell Ontology
  • 3.30pm Coffee
  • 4.00pm Yves Lussier / Andrea Califano (MAGNET)
  • 4.30pm Aris Floratis (MAGNET): BISON: The Bioinformatics Interface Structured Ontology
  • 5.00pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology

Wednesday October 31


  • 8.30am Continental Breakfast

Session III: Scientific Ontologies

  • Moderator: Zak Kohane (i2b2)
  • 9am
  • 10.30am Coffee
  • 11am


  • 12.45pm Lunch Break

Session IV: Ontologies for Cellular Networks (Part 2)

  • 2.00pm Alan Ruttenberg (Science Commons): The Ontology of Networks and Pathways: An Overview
  • 3.00pm TBD
  • 4.00pm Meeting Closes

Participants (Provisional List)

Robert Arp - NCBO, Buffalo, NY

Michael Ashburner - NCBO, Cambridge University Department of Genetics

Brian Athey - NCIBI, University of Michigan

Andrea Califano - MagNet, Columbia University, NY

Lindsay Cowell -- Duke University

Isaac Kohane -- i2b2 / Harvard University

Suzanna Lewis - NCBO, Berkeley, CA

Peter Lyster - NIH/NIGMS

Yves Lussier - MagNet, University of Chicago, IL

Chris Mungall -- NCBO, Berkeley, CA

[Representative] - PharmGKB, Stanford, CA

Alan Ruttenberg - Science Commons, Boston, MA

Karen Skinner - NIH/NIDA

Barry Smith - NCBO, Buffalo, NY

Balaji S. Srinivasan - Stanford, CA

David States + 1 further representative - NCIBI, University of Michigan

Ross Whitaker - NA-MIC, Utah



Hilton Hotel Newark Airport A block of rooms has been set aside for early registrants.

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