View source for Ontology of Networks and Pathways

== General Information == 

The [http://ncbo.us 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 ==

[http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Hotel Newark Airport] A block of rooms has been set aside for early registrants.

==Links ==

* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]

==Literature==

[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]