DiversityModule_Gramene-SAC_060110.ppt.pptVIP

Dan Born, Peter Bradbury, Ed Buckler Payan Canaran, Terry Casstevens, Dallas Kroon, Dave Matthews, Susan McCouch, Junjian Ni, Isaak Yosief Tecle, Doreen Ware, Immanuel Yap, Frank You, Ken Youens-Clark, Wei Zhao Current Status of Most Diversity Informatics Specific Aim #3: Develop data models and query tools to manage natural variation in monocot varietiesFinal Objectives for Nov 2007: Create data model Done; Revised in 2006; maize, wheat and rice proj. DBs live in Gramene Aid in curation Pedigree parser done; Excel upload for traits; project specific for other genotypes Interfaces Dataset download – Done (GDPC; web interfaces) Need to instantiate wheat and rice web interface Pedigree Display – Alpha Complete To do: Add trait and genotype Haplotype viewer – To Do GIS display – To Do 2005 Goals Fuse and instantiate project DBs into Gramene Complete upload tools; train key curators Complete GDPC browser; Complete Germinate connection; Write GRIN connection Start pedigree interface browser 1. Fuse and instantiate project DBs into Gramene DB revised in light of more input. Frozen in May 2005 Maize: Millions of curated phenotypic and genotypic data points have been included (Data from NSF “Maize molecular and functional diversity” project). Curator Qi Sun and Jeff Glaubitz Live through 1. Fuse and instantiate project DBs into Gramene Rice: Allelic data on 234 accessions with 169 genome-wide SSRs. Contains passport, taxonomic data, and links to IRRI/IRIS and GRIN. (Data from NRI Molecular Evaluation of Rice Germplasm using microsatellite markersproject) Curator: Isaak Yosief Tecle Wheat: 48 taxa and 6000+ SNP assays (Data from NSF “Haplotype polymorphism in polyploidy wheats and their diploid ancestors”) Curator: Frank You Live on dev site Gramene General Search Searches all tables for name or value Developed by Ken Youens-Clark On dev site. Panzea Web Interface Search by topic area SNP viewer Several outputs formats 2. Complete upload tools; train key curators Exc