Networks

Workshop on Ontologies of Cellular Networks

To ensure highly interactive and productive sessions, the number of workshop participants will be limited. If you are interested in participating, please contact: Barry Smith

The Workshop on Ontologies of Cellular Networks is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [1].

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 / University at Buffalo)

Gary Bader (BioPAX / University of Toronto)

Helen Berman (Protein Data Bank / Rutgers University)

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

Kei Cheung (Yale Center for Medical Informatics)

Lindsay Cowell (Infectious Disease Ontology / Duke University)

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

Peter D'Eustachio (Reactome / New York University)

Ken Ichiro Fukuda (INOH Pathway Database, Tokyo)

Louis Goldberg (Ontology Research Group / University at Buffalo)

Gopal Gopinathrao (Reactome / Cold Spring Harbor Laboratories)

Nancy Gough (Science)

Suzanna Lewis (NCBO / Lawrence Berkeley National Lab)

Joanne Luciana (BioPAX / Harvard Medical School)

Peter Lyster (NIGMS / National Institutes of Health)

Avi Ma'ayan (Mount Sinai School of Medicine)

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 (University of Chicago)

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

Richard Scheuermann (UTexas SW Medical Center at Dallas)

Stuart Sealfon (Mount Sinai School of Medicine)

Barry Smith (NCBO / University at Buffalo)

Andrea Splendiani (Medical Informatics, Rennes, France)

Cathy Wu (Protein Ontology / PIR, Georgetown University)

Venue

Hilton Newark Airport Hotel

Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make reservations either by calling 800-HILTONS and asking for the "National Center for Biomedical Ontology" block, or by entering group/convention code "NCB" when making reservations online at the Hilton Newark Airport Hotel website.

NOTE: To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than Wednesday, March 5. After this date, reservations will be accepted based on availability and at prevailing rates.

Links

• National Center for Biomedical Ontology

Literature

Current progress in network research

An Evaluation of Ontology Exchange Languages for Bioinformatics