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VBRC Group Meeting

January 25, 2008. VBRC Group Meeting. Current and Future. BRC Projects. Database. Database (CH). Indexing vgd_common (JM; 1Q) Fully implement Taxonomy tables (JO, DD; 2Q) Allow subspecies-level taxonomy Fix Dengue Fix HCV Fully update Pluto.vgd_common with all patches (CH). data.

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VBRC Group Meeting

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  1. January 25, 2008 VBRC Group Meeting

  2. Current and Future BRC Projects

  3. Database

  4. Database (CH) • Indexing vgd_common (JM; 1Q) • Fully implement Taxonomy tables (JO, DD; 2Q) • Allow subspecies-level taxonomy • Fix Dengue • Fix HCV • Fully update Pluto.vgd_common with all patches (CH)

  5. data

  6. Data (CH) • Data releases • Data Release 6.4 (JM; 1Q) • Data Release 6.5 (SC; 2Q) • Continuous data release (JM; 4Q) • Replication between Pluto and Gendb Databases • Automated annotation • Correct handling of “missing” information by web site

  7. Reference Genomes (CH) • Define • Curated strain • RefSeq strain • Links from all VOCs orthologs • Links to RefSeq and VBRC reference

  8. annotation

  9. BLAST (JM) • VBRC BLAST Processes (JM) • Reevaluate process of storing all BLAST data (2Q) • Separate BLAST data into new db (2Q) • Add views to vgd_common • Reassess BLAST XML Parsing tools • HCV BLAST (JO) • Update HCV BLAST db (1Q) • Move HCV BLAST from mars to VBRC (2Q)

  10. Protein information (JM, SC) • Generate all figures on-the-fly • Genome maps (1Q) • Hydrophobicity plots (3Q) • Get rid of dependence on GCG (3Q) • Display aa location of any motif hit (2Q) • Epitopes (SC) • Evaluate HCV epitopes: Why so many (JO) • Epitope identification by taxonomy (2Q) • EC numbers (SC; 2Q) • Polymerase • Protease

  11. HCV annotation (JO) • HCV genotyping • Alignments • Generate • View • Trees • Generate • View • Manual method for genotyping (2Q) • Automated genotyping (4Q)

  12. KDB (DD) • In production (1Q) • Tie in with vgd_common (2Q) • Table/field relationships • Annotation statistics updates

  13. UVic annotation pipeline (CH; 2Q) • VOCs • Better annotation • InterPro • Identify location • DO NOT delete genome/gene IDs

  14. Curation (EK; continuous) • Gene names • Consistent • Meaningful • Coordinate names in KDB with vgd_common (CH, DD)

  15. Controlled vocabularies (JO; 2008-2009) • GO • SO

  16. Tools

  17. Genome search and display(JO; 2008-2009) • New search interface • Combine genome and gene • Visualization • Genome maps • Search results • Variation • Features • Epitopes • Functional motifs

  18. Web Site

  19. Web site (JM) • Genome maps (1Q) • Create all on-the-fly • Add contract # to web site (1Q) • Update documents (1Q) • July 2007 Progress Report • Bug fixes (2Q) • How well do filters handle taxonomy updates/changes? (CH, DD; 2Q)

  20. help

  21. Help (JM, CG) • Online (1Q) • Tutorials (3Q)

  22. Outreach and collaboration

  23. IOWG (EJL, CH) • Annotation Lists (1Q) • GFF3 File formats (2Q) • Properly annotate mature peptides • Properly annotate RNA processing

  24. HCV (EJL) • Add LANL HCV advisory members to SWG (1Q) • Genome information (2Q) • Contact SLU for data

  25. ICTVdb (EJL) • Create link-outs (3Q)

  26. NCBI Interactions (CH) • Links • GenBank record parsing

  27. Next Group Meeting • February 8th, 2008 • 2:30 – 4:30 • AIDS Center Conference Room, BBRB Room 256A • Topic • KDB • Presenter • Don Dempsey

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