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Genetic Data in

The SAB 2008 report highlights significant progress in the growth of genetic and variation data at the University of British Columbia. Key achievements include the development of a comprehensive genetic map for C. elegans, improved collaboration through Gene Nameserver and variation curation, and the successful integration of data from multiple projects such as NemaGENETAG and the Knockout Consortium. Ongoing efforts focus on enhancing phenotype information, literature curation, and database improvement to facilitate international research collaboration and data sharing.

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Genetic Data in

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  1. Genetic Data in Mary Ann Tuli

  2. Growth of Genetic Data SAB 2008

  3. Growth in Variation Data - 1 SAB 2008

  4. Growth in Variation Data - 2 • 3500 have rich annotation • Description of lesion • Connection to sequence • Connection to strain • In maintenance SAB 2008

  5. Molecular Change Presentation SAB 2008

  6. Copy Number Variants • Generated by Comparative Genome Hybridization (CGH)‏ • The University of British of Columbia, Vancouver Gene Knockout Laboratory • 249 in WS190 • Displays region which is either definitely or probably deleted SAB 2008

  7. Growth in Variation Data - 1 SAB 2008

  8. Large Scale Allele Projects - developments • Phenotype information for NRBP alleles sent to CalTech • NemaGENETAG project data all submitted • CNV data from KO Consortium SAB 2008

  9. Genetic Map Data • We continue to receive data from web submission forms and publications • Acedb improvements • briggsae genetic map - Hillier SAB 2008

  10. Marey Maps for C. elegans SAB 2008

  11. Feature Curation • Will capture • Binding sites - Consensus sequences - Promoters • Literature curation (start up) • Request Tracker (RT) system • Model changes • ~60 pending papers SAB 2008

  12. Other Genomes – Tier II • Orthologs • connections stored in Geneace • names mainly automatically assigned • Nomenclature guidelines available in Wiki • Will update WormBook SAB 2008

  13. Nameservers • Eases site-to-site collaboration • Gene Nameserver • since 2006 • Pre-build checks & scripts • Variation Nameserver - test version available • Feature Nameserver • since 2007 • scripts SAB 2008

  14. Capturing Data • From Collaborators • In-house Web forms – NBP & NemaGENETAG • E-mail – KO Consortium • From Users • WormBase Submission forms • E-mail – genenames@wormbase • Within WormBase • E-mail – Jonathan & First Pass • Request Tracker (RT)‏ - Feature data • CalTech forms – Variation SAB 2008

  15. International Biocurator Society • Based in Geneva • ~13 databases • 3 conference calls • Wiki • Sub group formed to compose letter to journals asking for metadata. • Next meeting Spring 2009 - Germany SAB 2008

  16. Future Plans • Allele curation • Pre-2001 allele literature • Richer annotation of existing objects • Feature literature curation • Improved capture of data – CalTech • NemaGENETAG • Continued website display improvements SAB 2008

  17. Collaborators • Nomenclature • Jonathan Hodgkin • The CGC • Ann Rougvie & Theresa Stiernagle • The Knockout Consortium • Mark Edgley • Jeff Holmes • National BioResource Centre, Japan • Shohei Mitani • NemaGENETAG • Laurent Ségalat • Acedb SAB 2008

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