Gramene

Scientific Advisory Board MeetingSeptember 2003

Gramene Staff CSHL

Shuly Avraham Ken Clark Kiran Ratanapu Liya Ren Steve Schmidt Lincoln Stein Wei Xhao

Cornell Pankaj Jaiswal Susan McCouch Junjian Ni Immanuel Yap Greg Wilson

USDA Ed Buckler Doreen Ware

Gramene’s Specific Aims Migrate RiceGenes to a relational back

end. Curate major maps of rice, maize,

sorghum, wheat, barley & oats Generate comparative maps Curate rice mutants, strains,

phenotypes & QTLs Assign GO terms to 4000 rice proteins

Old Look

Gramene

New Look

Architecture

Internal Web Server External Web Server

Oracle ACeDB

EnsEMBLSchema

MapSchema

GOSchema

RiceGenesSchema

Firewall

Map Curation by SpeciesSpecies Map Sets

Rice 69

Maize 14

Sorghum 2

Barley 1

Oats 1

Wheat 1

Wild Rice 1

Map Curation by Type

Type Map Sets

Genetic 24

QTL 57

Physical (clone-based) 6

Sequence 2

Comparative Maps Correspondence table data model

Marker 1 <- Evidence -> Marker 2 Evidence types

Sequence similarity (auto) Marker name match (auto) Curation types

Hybridization Publication

The Matrix

Viewing Comparative Maps

Viewing Comparative Maps

Sequences Aligned to Rice (1)

Feature Name Total Features Distinct_mapped_features % of Total Features

Barley_est 370290 212378 57

Barley_GI 48122 23212 48

Barley_tug 53405 26282 49

Barley-consensus 21239 11045 52

Maize_BACend 25842 2338 9

Maize_consensus 10678 6771 63

Maize_est 211520 97182 45

Maize_GI 37344 17376 46

Maize_hi_cot 259452 40299 15

Maize_marker 4739 2023 42

Maize_meth_filt_CSHL/Mccombie 66390 11673 17

Maize_meth_filt_hi_cot_cluster 73262 13355 18

Maize_meth_filt_TIGR 117969 25367 21

Maize_meth_filt_TIGR_updated 251101 62640 24

Maize_Mu_insert 131364 16448 12

Maize_tug 41853 17956 42

Rice_BACend 88054 96016 81

Rice_cdna_clones 28469 21375 75

Sequences Aligned to Rice (2)Rice_CDS 1671 1252 74

Rice_est 201747 149226 73

Rice_GI 59934 30414 50

Rice_indica_clusters 24179 18812 77

Rice_indica_est 86623 59651 68

Rice_Markers 3965 3540 89

Rice_SSR 2416 2119 87

Rice_tos17_insert 4853 3990 82

Rice_tug 49619 25075 50

Sorghum_cluster_pratt 15499 7309 47

Sorghum_est 140260 78354 55

Sorghum_GI 23863 11947 50

Sorghum_gss_reads_klein 172 117 68

Sorghum_orion 100602 23942 23

Sorghum_tug 25190 12652 50

Wheat_est 428977 208442 48

Wheat_GI 109782 38900 35

Wheat_tug 107556 33652 31

Rice Mutant Curation

Mutant Page

QTL Curation

Ontologies Gene Ontology Plant Ontology

Anatomy Development

Trait Ontology

GO 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

Literature References

How are We Doing? Web User Survey, December 2002 120 page views 73 responses

RespondentsAffiliation

academic 54 75%non-profit 12 17%for-profit 6 8%

72

Positionresearcher/scientist 28 38%

postdoctoral 12 16%professor 8 11%graduate 20 27%

other 5 7%

73

UsageHow long have you used Gramene?1~2 years 287~12 months 211~6 months 15less than 1 month 17

How often to you use Gramene? daily 22weekly 34monthly 13occasionally 5first time 5

PrioritiesRice gene predictions [4.3]Rice genomic sequence [4.3]Genome comparisons among rice and other monocots [4.2]Rice genetic maps [4.1]Rice physical maps (Clone fingerprint maps) [4.1]Rice EST to rice genome alignments [4.0]Other monocot EST to rice genome alignments [3.9]Genetic marker assay information [3.9]Availability of clones and other reagents [3.8]Rice QTL information [3.8]Genetic and physical maps in other monocots [3.8]Availability of germplasm and strains [3.7]Genome comparisons among rice strains [3.7]Protein functional information (enzymatic acting, expression pattern, etc.) [3.6]Mutants and QTLs in other monocots [3.6]Rice mutant information [3.5]Rice SNPs [3.5]Expand scope of gramene to dicots [3.2]Other monocot SNPs [3.1]Protein phylogenetic information [3.1]

Suggestions“your site is fantastic! I expect that I will use it for all of my grass genomic , cdna search needs. thanks, and I'm glad I found it.”

“Keep up the good work. I would like to host the mirror site for India.”

“The site is extremely useful. Exhaustive data and information is available and links provided to access related data base. For rice workers it is boon to get into gramene to get any information on maps , markers, data, literatures etc. thank you and keep it up.”

More Suggestions“It would be very useful to have a (BLAST) searchable database of insertional mutants and information on obtaining those lines.”

“It is confusing that the details on the ENSEMBL browser only appear after extra cllicking - I still get confused about where things are in the 2 panels (top and bottom) that show since they seem so similar. Maybe a short hint about what is going on on each page or something?”

“Better manual pages. Though Gramene is MUCH more intuitive than many other genome browsers I spend (waste) alot of time clicking links just to see what they do in the hope they'll give me the result I'm looking for. The above suggestion may exemplify this confusion! For all I know (or don't know) the feature I suggest may already exist!”

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