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Gramene Scientific Advisory Board Meeting September 2003.

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Presentation on theme: "Gramene Scientific Advisory Board Meeting September 2003."— Presentation transcript:

1 Gramene Scientific Advisory Board Meeting September 2003

2 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

3 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

4 Old Look

5 Gramene

6 New Look

7 Architecture Internal Web Server External Web Server OracleACeDB EnsEMBL Schema Map Schema GO Schema RiceGenes Schema Firewall

8 Map Curation by Species SpeciesMap Sets Rice69 Maize14 Sorghum2 Barley1 Oats1 Wheat1 Wild Rice1

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

10 Comparative Maps  Correspondence table data model  Marker 1 Marker 2  Evidence types  Sequence similarity (auto)  Marker name match (auto)  Curation types  Hybridization  Publication

11 The Matrix

12 Viewing Comparative Maps


14 Sequences Aligned to Rice (1) Feature NameTotal FeaturesDistinct_mapped_features% of Total Features Barley_est37029021237857 Barley_GI481222321248 Barley_tug534052628249 Barley-consensus212391104552 Maize_BACend2584223389 Maize_consensus10678677163 Maize_est2115209718245 Maize_GI373441737646 Maize_hi_cot2594524029915 Maize_marker4739202342 Maize_meth_filt_CSHL/Mccombie663901167317 Maize_meth_filt_hi_cot_cluster732621335518 Maize_meth_filt_TIGR1179692536721 Maize_meth_filt_TIGR_updated2511016264024 Maize_Mu_insert1313641644812 Maize_tug418531795642 Rice_BACend880549601681 Rice_cdna_clones284692137575

15 Sequences Aligned to Rice (2) Rice_CDS1671125274 Rice_est20174714922673 Rice_GI599343041450 Rice_indica_clusters241791881277 Rice_indica_est866235965168 Rice_Markers3965354089 Rice_SSR2416211987 Rice_tos17_insert4853399082 Rice_tug496192507550 Sorghum_cluster_pratt15499730947 Sorghum_est1402607835455 Sorghum_GI238631194750 Sorghum_gss_reads_klein17211768 Sorghum_orion1006022394223 Sorghum_tug251901265250 Wheat_est42897720844248 Wheat_GI1097823890035 Wheat_tug1075563365231

16 Rice Mutant Curation

17 Mutant Page

18 QTL Curation

19 Ontologies  Gene Ontology  Plant Ontology  Anatomy  Development  Trait Ontology

20 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

21 Protein Page

22 Literature References

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

24 Respondents Affiliation academic5475% non-profit1217% for-profit68% 72 Position researcher/scientist2838% postdoctoral1216% professor811% graduate2027% other57% 73

25 Usage How long have you used Gramene? 1~2 years28 7~12 months21 1~6 months15 less than 1 month17 How often to you use Gramene? daily22 weekly34 monthly13 occasionally5 first time5

26 Priorities Rice 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]

27 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.”

28 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!”

29 Site Usage

30 Domains

31 Referrers

32 Referrers – no search engines

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