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

Agenda Template

Thursday, March 27, 2008

• 9.00am Registration and Continental Breakfast

• 10.00am: Session 1
• Moderator

Introductions

• 10am Participant Self-Introductions
• 10.15am Introduction to Ontology
• 10.45am Coffee
• 11.15am The OBO Foundry
• 11.45am

• 12.45pm Lunch

• 2.00-5.00pm Session 2
• Moderator:

Cellular Networks and Cellular Network Data

Friday, March 28, 2008

• 8.30am Continental Breakfast

• 9.00am Session 2
• Moderator:

Ontologies of Cellular Networks: Alternative Approaches

• Session 3

• 12.45pm Lunch Break

• Session 4

Ontologies of Cellular Networks: The Next Steps

• Moderator: Suzanna Lewis (NCBO, Berkeley)

• 2.00-4.00pm

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