Difference between revisions of "Ontology and Cellular Networks"

Revision as of 06:56, 12 September 2007

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/NLP 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

Ontology of Cellular Networks: Some Basic Ingredients

Moderator: Peter Lyster (NIH/NIGMS)

9am Participant Self-Introductions
9.15am Barry Smith (NCBO, Buffal): 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 October 31

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

Kei Cheung - Yale, CT

Lindsay Cowell - Duke University

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

@@ Line 28: / Line 28: @@
 * 10.45am   Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products
 * 11.15am   BioPAX/Reactome/TBD
 * 12.45pm   Lunch Break
@@ Line 49: / Line 50: @@
 *  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
+*  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