Gramene Scientific Advisory Board Meeting January 2005.

Gramene

Scientific Advisory Board MeetingJanuary 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 2000-2003

USDA CSREES/IFAFS + ARS 2003-2004

Bridge funding from NSF (continued ARS support)

2005-2007NSF + 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 curriculum @

highschool level Open source genome annotation pipeline

Old Look

New Look

New Look

Architecture

Internal Web Server External Web Server

Oracle

EnsEMBLSchema

MapSchema

OtherSchemas

Firewall

MySQL

Genome Annotation

Comparative Maps

NOEL UPDATE!Map Curation by SpeciesSpecies Map Sets

Rice 69

Maize 14

Sorghum 2

Barley 1

Oats 1

Wheat 1

Wild Rice 1

UPDATE! Map Curation by Type

Type Map Sets

Genetic 24

QTL 57

Physical (clone-based) 6

Sequence 2

COMPLETE!Sequences Aligned to Rice

Proteins cDNAs + ESTs Genomic Marker Gene EnrichedRice Japonica 25,835 293,657 25,706Rice Indica 87,668Rice Brachyantha 34,930Rice Nivara 76,621Rice Rufipogan 53,049Maize 230,245 73,397 32,294 300,532Barley 286,652Sorghum 167,754 117 743 35,346Wheat 376,460 3,442Ryegrass 15,103 58,075Sugarcane 141,702Millet 694

Total Sequences 25,835 1,599,935 296,189 62,185 335,878Total Bases ??? ??? ??? ??? ???

Mutant Curation

UPDATE! Curated Mutants & QTLs Curated Mutants XXX “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 curriculum @

highschool level Open source genome annotation pipeline