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Workshop on Ontologies of Cellular Networks

This NCBO 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].



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


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
Nancy Gough: Challenges to Representing Pathways
  • 11:00am Refreshment Break
  • 11:15am (Session 1, continued)
Richard Scheuermann: Biological Network Analysis and Representational Implications
Yves Lussier: Resources for Multiscale Analysis of Cellular Networks and ECM
  • 12:30pm Lunch Break
  • 1:30pm Session 2 - Introduction to Ontology (Moderator: Barry Smith)
Barry Smith: An Introduction to Biomedical Ontology
Lindsay Cowell: Using Ontologies to Represent Immunological Networks
Jose L. V. Mejino, Jr.: The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy
  • 3:30pm Refreshment Break
  • 3:45pm Session 3 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg)
Nigam Shah: Computations using pathways and networks
Andrea Splendini: Using BioPAX Computationally
  • 5:00pm End of Day 1

Friday, March 28, 2008

  • 8:30am Continental Breakfast
  • 9:00am Session 4: Current Approaches to Pathway and Network Ontologies (Moderator: Richard Scheuermann)
Markus Krummenacker: The BioCyc Ontologies
Ken Fukuda: The INOH Pathway Database: Curation, Annotation, Integration
Erick Antezana: The Cell Cycle Ontology
  • 10:30am Refreshment Break
  • 10:45am (Session 4, continued)
Peter D'Eustachio and Gopal Gopinathrao: Representing Biological Processes: The Reactome Database
Darren Natale: Protein Ontology: Addressing the Need for Precision in Representing Protein Networks
  • 12.30pm Lunch Break
  • 1:30pm Session 5 - Gaps in Pathway and Network Ontology (Moderator: Alan Ruttenberg)
Andrey Rzhetsky: Text-Mining & Ontologies
Oliver Ruebenacker: Systems Biology Pathway Exchange
Gopal Gopinathrao: Gaps in Reactome
Chris Sander: General Comments on Gaps between Pathways and Ontologies
Alan Ruttenberg: Some Gaps of My Own: BioPAX-OBO Relationship, Identity, Definition of 'Pathway', Declarative Representations, Falsifiability, Entities
Barry Smith: Pathways and Networks for Realists
Open discussion.
  • 4:00pm End of Day 2

Confirmed Participants

Erick Antezana (VIB / Ghent University, Belgium)

Mikel Egana Aranguren (University of Manchester, UK)

Robert Arp (NCBO / University at Buffalo)

Gary Bader (BioPAX / University of Toronto, Canada)

Michael Blinov (Center of Cell Analysis & Modeling / University of Connecticut Health Center)

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 Fukuda (INOH Pathway Database / Computational Biology Research Center, Advanced Industrial Science & Technology, Japan)

Louis Goldberg (Ontology Research Group / University at Buffalo)

Gopal Gopinathrao (Stein Lab / Cold Spring Harbor Laboratory)

Nancy Gough (Science Signaling, AAAS)

Matt Holford (Yale University)

Markus Krummenacker (SRI International)

Yves Lussier (University of Chicago)

Joanne S. Luciano (MITRE, BioPAX, BioPathways Consortium)

Peter Lyster (NIGMS / National Institutes of Health)

Avi Ma'ayan (Mount Sinai School of Medicine)

Jose 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 Modeling / 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)

Nigam Shah (NCBO / Stanford University)

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, Germany)

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

Venue / Lodging / Transportation

VENUE: The NCBO Workshop on Ontologies of Cellular Networks will take place on March 27-28, 2008 at the Hilton Newark Airport Hotel (Junior Ballroom).

LODGING: Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make room reservations either by calling 1-800-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.



HOTEL SHUTTLE: The Hilton Newark Airport Hotel provides complimentary shuttle service from (and to) the airport. When you arrive at the Newark Airport, follow signs to the Baggage Claim Area. Take the Airtrain to Airstation P4. The shuttle pickup is every 20 minutes from this location.

TAXI: Typical minimum charge is USD 20.00

DRIVING DIRECTIONS: Follow signs to airport exit, US Rte 1&9 N. to Haynes Ave. Take US Rte 1&9 S. After McClellan St. overpass, bear right to Service Road. The Hilton Hotel entrance is the 2nd driveway.


TRAVELLING SOUTHBOUND ON ROUTES 1 & 9: Local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.

TRAVELLING NORTHBOUND ON ROUTES 1 & 9: Exit at McClellan Street. At the base of the ramp, turn left, and the Hilton Hotel is on the right.

FROM THE N.J. TURNPIKE NORTHBOUND: Take exit 13A. Get on Routes 1 & 9 North to the McClellan Street exit. At base of ramp, turn left and the Hilton Hotel is on the right.

FROM THE N.J. TURNPIKE SOUTHBOUND: Take exit 14 to Routes 1 & 9 south, local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.



Addendum: Do Mountains Exist?

This paper:

Barry Smith and David M. Mark, “Do Mountains Exist? Towards an Ontology of Landforms”, Environment and Planning B (Planning and Design), 30(3) (2003), 411–427.

defends the thesis that mountains do indeed exist. But it argues that this assertion is non-trivial, in virtue of the fact that mountains have no determinate boundaries.

Similarly in the case of pathways and networks; pathways and networks do indeed exist -- but different groups of researchers place their boundaries in different places. To find ways to pool their data these different groups would need to acknowledge the differences in demarcation on which their pathway and network representations rest. See presentation Pathways and Networks for Realists.