Transcript "Big Data", Tree Fruit and the Genome Database for Rosaceae

“Big Data”, tree fruit and the
Genome Database for Rosaceae
Jim McFerson
Sook Jung
Ksenjia Gasic
Stephen Ficklin
Michael Coe
Dorrie Main
Washington State
Tree Fruit
Association
Wenatchee WA
5 Dec 2016
Modern ag research programs generate a lot of data!
Year after year after year……
“Big data” is high-volume, velocity and -variety information
assets that demand cost-effective,
innovative forms of information
processing for enhanced insight
and decision making.
What is GDR?
• Genome Database for Rosaceae
• Community database for worldwide Rosaceae
research community
• GDR initiated in 2003 to
– curate, house and integrate emerging Rosaceae
genomics, genetics and breeding data
– analyze complex data using high performance
computing and distill into usable data for researchers
– provide access to data mining tools
– facilitate comparative genomics within the family
• Model for generic database platform TRIPAL
GDR Home Page
www.rosaceae.org
GDR Vision Part 1
• Discovery
• Translation
• Application
Facilitate Rosaceae Research
• Highly engaged community (research and industry)
• Continuous funding since 2003
o USDA SCRI ($4.6M),
USDA NRSP10 ($2M)
o NSF PGRP ($4.6M)
o NSF DIBBS ($1.5 M)
o Industry ($1.75M)
o Land Grant Universities (salaries)
• Excellent development and curation team
Example of Current Breeders Resources
Community Data
WABP Private Data
Published Data
QTLs/MLTs/Markers
Crosses
Phenotype
Genotype
QTLs/MLTs
Markers
Associated data
RosBREED and
FruitBreedomics
curate and upload
upload
curate and upload
Private WABP Database in GDR
| browse | query | compare | download | upload | edit | output | cross assistance | convert markers |
State-of-the-Art Apple Breeding