Gramene - PowerPoint PPT Presentation

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Gramene
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Gramene

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  1. Gramene Scientific Advisory Board Meeting September 2003

  2. 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 Staff

  3. 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 Gramene’s Specific Aims

  4. Old Look

  5. Gramene

  6. New Look

  7. External Web Server Oracle ACeDB Internal Web Server Architecture Firewall RiceGenes Schema EnsEMBL Schema Map Schema GO Schema

  8. Map Curation by Species

  9. Map Curation by Type

  10. Comparative Maps • Correspondence table data model • Marker 1 <- Evidence -> Marker 2 • Evidence types • Sequence similarity (auto) • Marker name match (auto) • Curation types • Hybridization • Publication

  11. The Matrix

  12. Viewing Comparative Maps

  13. Viewing Comparative Maps

  14. Sequences Aligned to Rice (1)

  15. Sequences Aligned to Rice (2)

  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

  25. Usage How long have you used Gramene? 1~2 years 287~12 months 211~6 months 15less than 1 month 17How often to you use Gramene? daily 22weekly 34monthly 13occasionally 5first time 5

  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