Difference between revisions of "Networks"

Revision as of 08:29, 29 November 2007

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 27, 2008

9.00am Registration and Continental Breakfast

10.00am: Session 1

Ontologies of Cellular Networks: Some Basic Ingredients

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 BioPAX/Reactome/TBD

12.45pm Lunch Break

Afternoon

Thursday, March 28, 2008

8.30am Continental Breakfast

Ontology of Cellular Networks: Alternative Approaches

Session 3

12.45pm Lunch Break

Afternoon

Ontology of Cellular Networks: The Next Steps

Moderator: Suzanna Lewis (NCBO, Berkeley)

Meeting concludes at 4pm

Venue

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

Links

National Center for Biomedical Ontology

Literature

Current progress in network research

@@ Line 1: / Line 1: @@
 == Workshop on Ontologies of Cellular Networks ==
@@ Line 16: / Line 15: @@
 == Agenda Template ==
-'''Wednesday, March 26, 2008'''
+'''Wednesday, March 27, 2008'''
-Arrival
-'''Thursday, March 26, 2008'''
+* 9.00am Registration and Continental Breakfast
-''Morning''
+* 10.00am: Session 1
-* 8.30am Registration and Continental Breakfast
+'''Ontologies of Cellular Networks: Some Basic Ingredients'''
-'''Ontology of Cellular Networks: Some Basic Ingredients'''
-* Moderator: Peter Lyster (NIH/NIGMS)
 * 9am Participant Self-Introductions
@@ Line 32: / Line 27: @@
 *  9.45am   Lindsay Cowell (Duke): The Cell Ontology
 * 10.15am   Coffee
-* 10.45am   Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products
+* 10.45am   BioPAX/Reactome/TBD
-* 11.15am   BioPAX/Reactome/TBD
 * 12.45pm   Lunch Break
@@ Line 40: / Line 33: @@
 ''Afternoon''
-'''Constructing an Ontology of Cellular Networks'''
+'''Thursday, March 28, 2008'''
-* 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
+* Session 3
-*  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
@@ Line 72: / Line 47: @@
 * Moderator: Suzanna Lewis (NCBO, Berkeley)
-Session starts at 2pm
+Meeting concludes at 4pm
-== 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 ==