Networks
Workshop on Ontologies of Cellular Networks
General Information
The National Center for Biomedical Ontology will host a two-day workshop focused on ontologies of cellular networks.
Goals
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
Agenda Template
Wednesday, March 26, 2008 Arrival
Thursday, March 26, 2008
Morning
- 8.30am Registration and Continental Breakfast
Ontology of Cellular Networks: 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 Cellular Networks
- 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
Ontology of Cellular Networks: 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
Ontology of Cellular Networks: The Next Steps
- Moderator: Suzanna Lewis (NCBO, Berkeley)
Session starts at 2pm
Participants (Provisional List)
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
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.