Ontology of Networks and Pathways

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General Information

The National Center for Biomedical Ontology will host a two-day workshop focused on the ontology of networks and pathways. The meeting will be held in Newark NJ in March 2008.


The goals of this workshop are:

  • 1. to provide an introduction to the basic tools and methods of ontology
  • 2. to overview existing work on the ontology of networks and pathways with a view to enhanced coordination
  • 3. to foster networking among ontology developer and user groups in the field of networks and pathways

Rough Draft Agenda

Day 1


  • 8.30am Registration and Continental Breakfast

Ontology of Networks and Pathways: Some Basic Ingredients

  • Moderator: Peter Lyster (NIH/NIGMS)
  • 9am Participant Self-Introductions
  • 9.15am Barry Smith (NCBO, Buffalo): What is a Network?
  • 9.45am Lindsay Cowell (Duke): The Cell Ontology
  • 10.15am Coffee
  • 10.45am Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products
  • 11.15am BioPAX/Reactome/TBD
  • 12.45pm Lunch Break


Constructing an Ontology of Networks and Pathways

  • Moderator: Alan Ruttenberg (Science Commons / Semantic Web HCLSIG)

This will be an interactive hands-on session, in which data annotation needs will be presented, on the basis of which the attempt will be made to construct the beginnings of a cellular network ontology.



  • 8.30am Continental Breakfast

Alternative Approaches

  • Moderator: TBD
  • 9.00am Aris Floratos (MAGNET, Columbia University): BISON - The Bioinformatics Interface Structured Ontology
  • 9.30pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology
  • 10.00am TBD
  • 10.30am Coffee
  • 11.00am Yves Lussier (Chicago): Integrating the Cell Ontology with other Ontologies and with Text - Bridging the Modeling Gap
  • 11.30am Discussion on Statistical/NLP vs. Manual Approaches to Ontology Construction
  • 12.45pm Lunch Break


The Next Steps

  • Moderator: Suzanna Lewis (NCBO, Berkeley)

Session starts at 2pm

Potential Participants

Robert Arp - NCBO, Buffalo, NY

Michael Ashburner - NCBO, Cambridge University Department of Genetics

Ed Barbour - Rockefeller University

Werner Ceusters - University at Buffalo

Kei Cheung - Yale, CT

Lindsay Cowell - Duke University

Peter D'Eustachio - Reactome

Marc Halfon - Buffalo

Nick Khazanov - Rockefeller University

Natasha Lenkova - Rockefeller University

Suzanna Lewis - NCBO, Berkeley, CA

Peter Lyster - NIH/NIGMS

Yves Lussier - MagNet, University of Chicago, IL

Avi Ma'ayan - Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine

Chris Mungall -- NCBO, Berkeley, CA

Alan Ruttenberg - Science Commons, Boston, MA

Nigam Shah - NCBO, Stanford, CA

Karen Skinner - NIH/NIDA

Barry Smith - NCBO, Buffalo, NY

Balaji S. Srinivasan - PharmGKB, Stanford, CA

David States - NCIBI, University of Michigan

Ross Whitaker - NA-MIC, Utah


Hilton Hotel Newark Airport A block of rooms has been set aside for early registrants.



Current progress in network research

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