1. January 25, 2008

2. Current and Future

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)

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

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

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

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)

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

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 8 th, 2008  2:30 – 4:30  AIDS Center Conference Room, BBRB Room 256A  Topic  KDB  Presenter  Don Dempsey