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Gramene

Gramene. Scientific Advisory Board Meeting January 2005. 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

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Gramene

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  1. Gramene Scientific Advisory Board Meeting January 2005

  2. 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 Gramene Staff

  3. A Brief History • 2000-2003USDA CSREES/IFAFS + ARS • 2003-2004 Bridge funding from NSF (continued ARS support) • 2005-2007NSF + ARS

  4. 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 CSREES

  5. 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 curriculum @ highschool level • Open source genome annotation pipeline

  6. Old Look

  7. New Look

  8. New Look

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

  10. Genome Annotation

  11. Comparative Maps

  12. NOEL UPDATE!Map Curation by Species

  13. UPDATE! Map Curation by Type

  14. COMPLETE!Sequences Aligned to Rice

  15. Mutant Curation

  16. UPDATE! Curated Mutants & QTLs • Curated Mutants XXX • “Phase I” QTLs • Studies XXX • Traits XXX

  17. QTL Curation

  18. 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

  19. Protein Page

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

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