Presentation on theme: "GDR, the Genome Database for Rosaceae, in Chado and Tripal Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Sushan Ru, Ping Zheng,"— Presentation transcript:
GDR, the Genome Database for Rosaceae, in Chado and Tripal Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Sushan Ru, Ping Zheng, Jing Yu, Aureliano Bombarely, Sushan Ru, Kate Evans, Cameron Peace, Albert Abbott, Lukas Mueller, Mercy Olmstead, Dorrie Main
Introduction Genomic, Genetic and Breeding database for Rosaceae community (12 years!) Genetics Breeding GermplasmDiversity Genomics Integrated Data & Tools
What’s New - platform Converted to use open source tools for an efficient and flexible database construction Completely in Chado! New and improved search sites and data pages in Tripal Content Management System Chado Generic Database schema Drupal modules as web front-end for Chado
What’s New – data and functionality Genomics EST Unigenes NCBI Data (Gene search site) WGS and annotation (Pear WGS data!) Synteny data Pathway data Genetics Markers and maps QTL/Molecular diversity New search/detail page in Tripal! Breeding Genotypic data Phenotypic data Germplasm data New Tool – Sequence retrieval tool New tutorials!
GDR Demo Species/Genome Pages New Tripal pages for gene, sequence, marker, QTL, diversity and publication data New tool for sequence retrieval Breeding data and tools
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.Continue to add more genetic and genomic data 2.Facilitate community gene annotation by building online gene curation pages. 3.Develop breeders toolbox in Tripal 4.Further develop online tools to aid Marker Assisted Breeding.
Acknowledgements GDR team members Taein Lee Stephen Ficklin ChunHuai Cheng Ping Zheng Anna Blenda Sushan Ru Dorrie Main Jing Yu 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