Ontology of Networks and Pathways
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.
Goals
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
Morning
- 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
Afternoon
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.
Wednesday
Morning
- 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
Afternoon
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
Venue
Hilton Hotel Newark Airport A block of rooms has been set aside for early registrants.