vbrc group meeting
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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January 25, 2008
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Current and Future
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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)
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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
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Reference Genomes (CH)
Define Curated strain RefSeq strain
Links from all VOCs orthologs Links to RefSeq and VBRC reference
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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)
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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
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HCV annotation (JO)
HCV genotyping Alignments
Generate View
Trees Generate View
Manual method for genotyping (2Q) Automated genotyping (4Q)
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KDB (DD)
In production (1Q) Tie in with vgd_common (2Q)
Table/field relationships Annotation statistics updates
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UVic annotation pipeline (CH; 2Q) VOCs
Better annotation InterPro
Identify location DO NOT delete genome/gene IDs
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Curation (EK; continuous) Gene names
Consistent Meaningful Coordinate names in KDB with
vgd_common (CH, DD)
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Controlled vocabularies (JO; 2008-2009) GO SO
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Genome search and display(JO; 2008-2009) New search interface
Combine genome and gene Visualization
Genome maps Search results Variation Features
Epitopes Functional motifs
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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)
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Help (JM, CG)
Online (1Q) Tutorials (3Q)
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IOWG (EJL, CH)
Annotation Lists (1Q) GFF3 File formats (2Q)
Properly annotate mature peptides Properly annotate RNA processing
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HCV (EJL)
Add LANL HCV advisory members to SWG (1Q)
Genome information (2Q) Contact SLU for data
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ICTVdb (EJL)
Create link-outs (3Q)
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NCBI Interactions (CH)
Links GenBank record parsing
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Next Group Meeting
February 8th, 2008 2:30 – 4:30 AIDS Center Conference Room, BBRB
Room 256A Topic
KDB Presenter
Don Dempsey