Ontology and Cellular Networks

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.

Goals

The goals of this workshop are:

• 1. to provide an introduction to the basic tools and methods of ontology
• 2. to take the first steps towards developing an ontology of cellular networks.
• 3. to address alternative approaches to ontology construction, with an emphasis on statistical vs. manual approaches
• 4. to foster networking between ontology developer groups in the field of biomedical informatics

Agenda

Tuesday October 30

Morning

• 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 (NCIBI)
• 9.45am Chris Mungall (NCBO)
• 11.15am Coffee
• 11.30am Aris Floratos (MAGNET
• Representatives from other NCBCs

Afternoon

• 12.45pm Lunch Break

Session II: Ontologies for Cellular Networks (Part 1)

• Moderator: Andrea Califano (MAGNET, Columbia University)
• 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 (MAGNET): Integrating the Cell Ontology with other Ontologies and with Text - Bridging the Modeling Gap
• 4.30pm Aris Floratos (MAGNET, Columbia University): BISON - The Bioinformatics Interface Structured Ontology
• 5.00pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology

Wednesday October 31

Morning

• 8.30am Continental Breakfast

Session III: Scientific Ontologies

• Moderator: Zak Kohane (i2b2)

• 9am
• 10.30am Coffee
• 11.00am

Afternoon

• 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

Ed Barbour - Rockefeller University

Andrea Califano - MagNet, Columbia University, NY

Kei Cheung - Yale, CT

Lindsay Cowell - Duke University

Nick Khazanov - Rockefeller University

Isaac Kohane - i2b2 / Harvard University

Natasha Lenkova - Rockefeller University

Suzanna Lewis - NCBO, Berkeley, CA

Peter Lyster - NIH/NIGMS

Yves Lussier - MagNet, University of Chicago, IL

Avi Ma'ayan - Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine

Chris Mungall -- NCBO, Berkeley, CA

Alan Ruttenberg - Science Commons, Boston, MA

Nigam Shah - NCBO, Stanford, CA

Karen Skinner - NIH/NIDA

Barry Smith - NCBO, Buffalo, NY

Balaji S. Srinivasan - PharmGKB, Stanford, CA

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

Ross Whitaker - NA-MIC, Utah

CCB ?

Venue

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

Links

National Centers for Biomedical Computing

• National Center for Biomedical Ontology

• National Center for the Multi-Scale Analysis of Genomic and Cellular Networks

• Center for Computational Biology

• Informatics for Integrating Biology and the Bedside

• National Alliance for Medical Imaging Computing

• Physics-based Simulation of Biological Structures

• National Center for Integrative Biomedical Informatics

Ontology Working Group

Literature

Current progress in network research