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

This workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It 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

Potential topics for discussion include:

• signalling pathways
• metabolic pathways
• regulatory networks
• interaction networks
• gene expression correlation networks
• physiological networks
• neurocurrent networks

Preliminary Agenda

Thursday, March 27, 2008

• 9:00am Registration and Continental Breakfast

• 9:30am Participant Self-Introductions

• 10:00am Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)

Chris Sander: Pathways and Networks: An Overview of the Science

Nigam Shah (Stanford/NCBO): Requirements for representing biological processes as Pathways and Networks

• 11:00am Refreshment Break

• 11:15am (Session 1, contd.)

Darren Natale (Georgetown): The Protein Ontology and Cellular Networks

Yves Lussier (MAGNET): The Extracellular Matrix

• 12:30pm Lunch Break

• 1:30pm Session 2 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg)

Presenters will include:

Richard Scheuermann: Networks and Modularity

Andrea Splendini: Using BioPAX Computationally

• 3:30pm Refreshment Break
• 3:45pm Session 3 - Introduction to Ontology (Moderator: Barry Smith)

Presenters will include

Lindsay Cowell: Immune System Ontology

J. L. V. Mejino, Jr.: FMA: Framework for Subcellular Network Anatomy

Barry Smith: Pathways and Networks for Realists

• 5:00pm End of Day 1

Friday, March 28, 2008

• 8:30am Continental Breakfast

• 9:00am Session 4: Current Approaches to Pathway and Network Ontologis (Moderator: Richard Scheuermann)

Peter d'Eustachio: Reactome

Ken Fukuda: The INOH Pathway Database

• 10:45am Refreshment Break
• 11:00am (Session 4, contd.)

• 12.30pm Lunch Break

• 1:30 Session 5 - Gaps in Network Ontology (Moderator: Alan Ruttenberg)

Balaji S. Srinivasan

Gopal Gopinathrao: Gaps in Reactome

Open discussion; presenters and topics to be decided

• 4:00pm End of Day 2

Participants

Prospective Participants:

(**CONFIRMED)

Erick Antezana (VIB / Ghent University)**

Mikel Egana Eranguren (University of Manchester)**

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 University / Center for Medical Informatics)**

Lindsay Cowell (Infectious Disease Ontology / Duke University Medical Center)**

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

Peter D'Eustachio (Reactome / New York University School of Medicine)**

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 Signaling, AAAS)**

Matt Holford (Yale University)**

Joanne Luciano (BioPAX / MITRE)

Yves Lussier (University of Chicago)**

Peter Lyster (NIGMS / National Institutes of Health)**

Avi Ma'ayan (Mount Sinai School of Medicine)**

J. L. V. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)**

Richard Morse (CHDI Management Inc. / CHDI Foundation Inc.)**

Josefina (Fina) Nash (Coriell Institute)**

Darren Natale (Protein Ontology / PIR, Georgetown University Medical Center)**

Elgar Pichler (BioPAX / AstraZeneca)**

Othel Rolle (Pfizer, Inc.)**

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 (UT Southwestern Medical Center at Dallas)**

Stuart Sealfon (Mount Sinai School of Medicine)

Barry Smith (NCBO / University at Buffalo)**

Andrea Splendiani (BioPAX/Medical Informatics, University of Rennes, France)**

Balaji S. Srinivasan (Stanford University, Statistics)**

John Westbrook (Rutgers)**

Ulrike Wittig (EML Research gGmbH)**

Cathy Wu (Protein Ontology / PIR, Georgetown University Medical Center)**

Venue / Hotel Reservations

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

• FMA: Foundational Model of Anatomy

• National Center for Biomedical Ontology

• OBO Foundry

Literature

Current progress in network research

An evaluation of ontology exchange languages for bioinformatics

Coordinated Evolution of Ontologies to Support Biomedical Data Integration