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[Arabidopsis] Arabidopsis database update: New Funding for Portal and for International Contributors

Joanna Friesner via arab-gen%40net.bio.net (by jdfriesner from ucdavis.edu)
Wed Oct 23 17:58:48 EST 2013


* A new article entitled ŒArabidopsis Data Gets New Home at JCVI©ös AIP as
TAIR Turns to Subscriptions to Stay Afloat
(http://www.arabidopsisinformatics.org/wp-content/uploads/2013/09/BI_AIP_TA
IR_Sept2013.pdf) by Uduak Grace Thomas
describes the three+ year process by members of the international
Arabidopsis community to
(1) maintain continuity in housing vital Arabidopsis data
(2) expand capabilities to store and manage vast new datasets and
datatypes 
(3) develop new resources and integrate resources developed (or to be
developed) by the global community and
(4) engage a wider range of researchers, funding agencies and countries in
support of vital community resources.
These efforts culminated recently in an NSF award to PI Chris Town (J.
Craig Venter Institute) to develop a
new Arabidopsis Information Portal (AIP). Town and colleagues from the
Texas Advanced Computing Center and
Cambridge University expect to produce a functioning portal prototype in
the coming months. 
The project will leverage significant NSF investments in plant
bioinformatics via the iPlant Collaborative.
It will also sub-contract with TAIR staff to migrate existing data into an
open source relational database.

**Community outreach:
(1) A community workshop
(https://pag.confex.com/pag/xxii/webprogram/Session2169.html) to
discuss the Arabidopsis Information Portal (AIP) and the International
Arabidopsis Informatics Consortium (IAIC)
will be held on January 13th during the 2014 Plant and Animal Genome
meeting in San Diego, CA.
(2) Additional IAIC/AIP community workshops are being planned in
conjunction with the 2014 International Conference on Arabidopsis Research
(ICAR): July 28-August 1 at the University of British Columbia in
Vancouver, Canada.

***Community connections to the new AIP:
Several groups in other countries have recently been funded to contribute
towards the AIP including:
(3) Genome Canada funding to Nicholas Provart and colleagues to develop 7
modules based on the Bio-Analytic Resource (BAR),
(4) German BMBF funding to Bjoern Usadel at the RWTH to make MapMan and
other data sets from the GabiPD available,
(5) UK BBSRC funding to Sean May at Nottingham to develop a Stock Center
module.

****AIP Structure: The AIP will be structured in three tiers including a
user interface, a database structure, and a
web-services layer that will pull information from JCVI-hosted data
warehouses and external databases through third-party applications.

*****AIP development plans include:
- An implementation of an Arabidopsis-specific instance of InterMine, a
data integration platform
that is widely accepted in the animal model organism database community
- The design and construction of a web services layer that facilitates
data access
- Integration with iPlant Collaborative resources
- Federation with other data providers
- Development of analytical workflows

The article by U. Thomas also describes the new subscription model planned
by TAIR staff and differences between the two resources:
(http://www.arabidopsisinformatics.org/wp-content/uploads/2013/09/BI_AIP_TA
IR_Sept2013.pdf)

IAIC community website: http://www.arabidopsisinformatics.org

IAIC Interim Director: Blake Meyers, University of Delaware
-- 
Joanna Friesner Ph.D.

NAASC Coordinator
IAIC Assistant
ICAR 2014 Coordinator
Jdfriesner from ucdavis.edu

ICAR 2014, The 25th International Conference on Arabidopsis Research
Organized by the North American Arabidopsis Steering Committee
July 28-Aug. 1, 2014
University of British Columbia
Vancouver, Canada





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