Gramene Scientific Advisory Board Meeting January 2005

Gramene Staff  CSHL  Shuly Avraham (1/2)  Payan Canaran (1/2)  Ken Clark  Chengzhi Liang  Kiran Ratanapu  Liya Ren  Steve Schmidt  Will Spooner (1/2)  Lincoln Stein  Wei Xhao (1/2)  Cornell  Pankaj Jaiswal  Molly Fogleman  Susan McCouch  Junjian Ni  Immanuel Yap  Greg Wilson  USDA  Ed Buckler  Terry Casstevens  Doreen Ware

A Brief History  USDA CSREES/IFAFS + ARS  Bridge funding from NSF (continued ARS support)  NSF + ARS

Specific Aims Under CSREES  Migrate RiceGenes to a relational back end.  Curate major maps of rice, maize, sorghum, wheat, barley & oats  Generate comparative maps among cereals  Curate rice mutants, strains, phenotypes & QTLs  Assign GO terms to rice proteins

Specific Aims Under NSF  All previous aims, plus…  High density maize/rice comparative map  Diversity module  QTL & diversity modules  Advanced query tool (BioMart)  Genome annotation highschool level  Open source genome annotation pipeline

Old Look

New Look

Architecture Internal Web Server External Web Server Oracle EnsEMBL Schema Map Schema Other Schemas Firewall MySQL

Genome Annotation

Comparative Maps

NOEL UPDATE! Map Curation by Species SpeciesMap Sets Rice69 Maize14 Sorghum2 Barley1 Oats1 Wheat1 Wild Rice1

UPDATE! Map Curation by Type TypeMap Sets Genetic24 QTL57 Physical (clone-based)6 Sequence2

COMPLETE! Sequences Aligned to Rice

Mutant Curation

UPDATE! Curated Mutants & QTLs  Curated MutantsXXX  “Phase I” QTLs  Studies XXX  Traits XXX

QTL Curation

UPDATE! Protein Curation  Proteins from SwissProt/TREMBL  Annotated with  Pfam, prosite, TMHMM, SignalP, Predotar  Associated to GO with Interpro2GO  Associations manually reviewed  14,708 proteins assigned  13,319 proteins reviewed  16,722 of 35,065 associations reviewed

Protein Page

Specific Aims Under NSF  High density maize/rice comparative map  Diversity module  QTL & phenotype modules  Advanced query tool (BioMart)  Genome annotation highschool level  Open source genome annotation pipeline