Ontology and Cellular Networks

General Information

- - -Ontology of Networks and Pathways - - - - -

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PLEASE NOTE THAT THIS MEETING HAS BEEN POSTPONED. FURTHER DETAILS WILL FOLLOW

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The National Center for Biomedical Ontology will host a two-day workshop focused on ontology and cellular networks.

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/NLP vs. manual approaches
• 4. to foster networking between ontology developer groups in the field of biomedical informatics

Agenda

Tuesday

Morning

• 8.30am Registration and Continental Breakfast

Ontology of Cellular Networks: Some Basic Ingredients

• Moderator: Peter Lyster (NIH/NIGMS)

• 9am Participant Self-Introductions
• 9.15am Barry Smith (NCBO, Buffalo): What is a Network?
• 9.45am Lindsay Cowell (Duke): The Cell Ontology
• 10.15am Coffee
• 10.45am Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products
• 11.15am BioPAX/Reactome/TBD

• 12.45pm Lunch Break

Afternoon

Constructing an Ontology of Cellular Networks

• Moderator: Alan Ruttenberg (Science Commons / Semantic Web HCLSIG)

This will be an interactive hands-on session, in which data annotation needs will be presented, on the basis of which the attempt will be made to construct the beginnings of a cellular network ontology.

Wednesday

Morning

• 8.30am Continental Breakfast

Ontology of Cellular Networks: Alternative Approaches

• Moderator: TBD

• 9.00am Aris Floratos (MAGNET, Columbia University): BISON - The Bioinformatics Interface Structured Ontology
• 9.30pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology
• 10.00am TBD
• 10.30am Coffee
• 11.00am Yves Lussier (Chicago): Integrating the Cell Ontology with other Ontologies and with Text - Bridging the Modeling Gap
• 11.30am Discussion on Statistical/NLP vs. Manual Approaches to Ontology Construction

• 12.45pm Lunch Break

Afternoon

Ontology of Cellular Networks: The Next Steps

• Moderator: Suzanna Lewis (NCBO, Berkeley)

Session starts at 2pm

Participants (Provisional List)

Robert Arp - NCBO, Buffalo, NY

Michael Ashburner - NCBO, Cambridge University Department of Genetics

Ed Barbour - Rockefeller University

Werner Ceusters - University at Buffalo

Kei Cheung - Yale, CT

Lindsay Cowell - Duke University

Marc Halfon - Buffalo

Nick Khazanov - Rockefeller 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 - NCIBI, University of Michigan

Ross Whitaker - NA-MIC, Utah

Venue

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

Links

• National Center for Biomedical Ontology

Literature

Current progress in network research