Transcript Computer demo - the Genome Database for Rosaceae

New Data and Functionality of GDR,
the Genome Database for Rosaceae
Sook Jung, Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Ping Zheng, Anna
Blenda, Sushan Ru, Kate Evans, Cameron Peace, Nnadozie Oraguzie,
Albert Abbott, Desmond Layne, Mercy Olmstead, Frederick Gmitter,
Chunxian Chen, Lukas Mueller, Dorrie Main
Introduction
•
•
Genomic, Genetic and Breeding database for
Rosaceae community (11 years!)
Built using open source tools for an efficient and
flexible database construction
Content Management System
Drupal modules as web front-end for Chado
Stephen Ficklin, GMOD workshop, Wed 11:50 AM
Chado
Generic Database schema
New Data and Functionality
• Genomics
Genomics
Genetics
Integrated
Data & Tools
Diversity
Germplasm
Breeding
• EST Unigene V5
• NCBI data
• WGS and annotation
(More annotation and
Search tools)
• Synteny data
• Pathway data
• RosaR80 data
• Genetics
•
•
Markers and maps
QTL/Molecular diversity
• Breeding
• Genotypic data
• Phenotypic data
• Germplasm data
(Enhanced interface)
Species page
5
6
Search for genes (from WGS or NCBI) and unigene
8
Gene Search Results
9
Pathway Tools
(PeachCyc, FragariaCyc and AppleCyc)
Pathway Tools cont.
Comparison between MetaCyc and KEGG
http://biocyc.org/metacyc/MetaCycUserGuideNew.shtml
Search for syntenic regions using Gbrowse_Syn
Phenotyping Data Search
13
14
Variety Detail Page
Genotypic data search
16
Generate Input files for Pedimap, a breeding
software
CrossAssist: Generates a list of parents and the number
of seedlings to get the progeny with desired traits
Current Objectives
1.Integrate more genetic data (marker, QTL, maps)
and association with Trait Ontology (developing
Rosaceae Trait Ontology)
2.Continue to integrate NCBI sequences
3.Develop new and improved search sites and data pages
in Tripal
4.Growers Gateway where growers can view and compare
cultivar performance data.
Acknowledgements
• GDR team members
Dorrie Main
Taein Lee Stephen Ficklin Jing Yu ChunHuai Cheng Ping Zheng Anna Blenda Sushan Ru
• Project coPIs- Dorrie Main (PI), Bert Abbott, Cameron Peace, Kate
Evans, Des Layne, Nnadozie Oraguzie, Mercy Olmstead, Fred Gmitter
Jr., the RosBREED teams
• Rosaceae and Bioinformatics Community 
• USDA NIFA SCRI, NSF Plant Genome Program, MARS, USDA-ARS,
Washington Tree Fruit Research Commission, WSU, Clemson
University, University of Florida, Boyce Thompson Institute