Networks

Goals

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

The goals of this workshop are:

• 1. to provide an introduction to the basic tools and methods of ontology
• 2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks
• 3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail
• 4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data

Preliminary Agenda

Thursday, March 27, 2008

• 9:00am Registration and Continental Breakfast

• 10:00am Session 1 - Introductions

Moderator:

• 10:00am Participant Self-Introductions
• 10:15am Introduction to Ontology
• 10:45am The OBO Foundry
• 11:15am Refreshment Break
• 11:45am

• 12:45pm Lunch Break

• 2:00pm Session 2 - Cellular Networks and Cellular Network Data

Moderator:

• 3:15pm Refreshment Break

• 5:00pm End of Day 1

Friday, March 28, 2008

• 8:30am Continental Breakfast

• 9:00am Session 3 - Ontologies of Cellular Networks: Alternative Approaches

Moderator:

• 10:45am Refreshment Break

• Session 4 -

Moderator:

• 12:45pm Lunch Break

• 2:00 Session 5 - Ontologies of Cellular Networks: The Next Steps

Moderator: Suzanna Lewis (NCBO, Berkeley)

• 4:00pm End of Day 2

Participants

Participants will include:

Robert Arp (NCBO / Buffalo)

Gary Bader (BioPAX / University of Toronto)

Helen Berman (PDB / Ruttgers)

William Bug (BIRN Ontology Task Force, UC San Diego)

Werner Ceusters (Ontology Research Group, University at Buffalo)

Lindsay Cowell (Infectious Disease Ontology / Duke University)

Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)

Peter D'Eustachio (Reactome / New York University)

Ken Fukuda (INOH / Tokyo)

Gopal Gopinathrao (Reactome / Cold Spring Harbor Laboratories)

Nancy Gough (Science)

Suzanna Lewis (NCBO, Berkeley)

Joanne Luciana (BioPAX / Harvard Medical School)

Peter Lyster (NIH / NIGMS)

Avi Ma'ayan (Mount Sinai, NY)

J. L. E. Mejino, Jr. (FMA Ontology, University of Washington, Seattle)

Darren Natale (Protein Ontology/PIR, Georgetown University)

Oliver Ruebenacker (Center for Cell Analysis and Modelling / University of Connecticut Health Center)

Alan Ruttenberg (BioPAX / Science Commons)

Andrey Rzhetsky (Chicago)

Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)

Richard Scheuermann (UTexas SW Medical Center)

Stuart Sealfon (Mount Sinai, NY)

Barry Smith (NCBO / Buffalo)

Andrea Splendiani (Medical Informatics, Rennes, France)

Cathy Wu (Protein Ontology/PIR, Georgetown University)

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

An Evaluation of Ontology Exchange Languages for Bioinformatics