WormBase and the CGC

1. WormBase and the CGC Mary Ann Tuli Advisory Board Meeting, CSHL 2005

2. Growth of genetic data Advisory Board Meeting, CSHL 2005

3. WBGene • ?Gene model introduced in April 2004 (WS124) • Name server – streamlining gene tracking Advisory Board Meeting, CSHL 2005

4. Gene Classes • 200 classes with no members • 1692 CGC names not connected to sequences • let and seven TM receptors are largest gene classes Advisory Board Meeting, CSHL 2005

5. CGC Gene Names Advisory Board Meeting, CSHL 2005

6. Gene Naming Pipeline CGC E-mail Geneace Curator Submitter Web Form Advisory Board Meeting, CSHL 2005

7. Developments – Tracking gene names Before: Gene_name: abu-1 Gene_class: abu-1 Other_name: pqn-1 Remark“pqn-1 is Other_name of abu-1 and has been merged into it” After: Gene_name: abu-1 Gene_class: pqn Other_name: pqn-1Old_member: pqn-1 Gene_name: pqn-1 Former_member_of: pqn Advisory Board Meeting, CSHL 2005

8. Developments – Tracking gene names • Former_member_of and Old_member introduced in WS144 • WS150 = 663 CGC Other_names in 291 gene classes Advisory Board Meeting, CSHL 2005

9. Developments - Status • Before: • Live tag only in ?Gene model • Absence implied object was Dead • Difficult to differentiate between different statuses Advisory Board Meeting, CSHL 2005

10. Developments - Status • After: • Status tag introduced in Gene and Variation model (WS144) • Live, Dead or Suppressed Advisory Board Meeting, CSHL 2005

11. The Variation Class Locus Class Allele Class VariationClass WS140 Advisory Board Meeting, CSHL 2005

12. The Variation Class • Type of Variation • Deletion • Insertion_and_deletion • Insertion • Substitution • Mos_insertion • Transposon_insertion • SNPs Advisory Board Meeting, CSHL 2005

13. Growth in Allele Data • Nearly 10,000 manually curated alleles • Most have at least a gene connection • Many have details of the strain carrying the mutation • 1500 have rich annotation • Description of lesion • Connection to sequence • Submission of Plasterk high throughput chemical mutagenesis/sequencing will result in many new alleles Advisory Board Meeting, CSHL 2005

14. Allele Submission Pipeline E-mail Geneace Curator NBP Submitter Web Form Advisory Board Meeting, CSHL 2005

15. Knockout Alleles • Mark Edgley • Jeff Holmes Advisory Board Meeting, CSHL 2005

16. Knockout Alleles • Shohei Mitani NBP Advisory Board Meeting, CSHL 2005

17. Knockout Alleles - plans • Possible Web form for collaborators to upload data • Advantages • onus on user to provide accurate data • More efficient way for us to convey changes in database conventions Advisory Board Meeting, CSHL 2005

18. Strain Data • Sent periodically to WormBase from Theresa Stiernagle • Leads to merges of Gene names and sequences • Leads to updates of tag- genes Advisory Board Meeting, CSHL 2005

19. Strain Data – tag gene class • All genes with KO alleles should have name which follows recommendations e.g. unc-12 not R09B3.4 • tag- genes assigned…but the list kept growing • No longer assign new tag- genes Advisory Board Meeting, CSHL 2005

20. Laboratory Data • Laboratory data sent from the CGC and Caltech Advisory Board Meeting, CSHL 2005

21. Multipoint Data • Process of adding inferred multi_pt_data continues • Script in Jan 2004 to add inferred data. • 1996 ~1,300 genetic marker loci • Mar 2004 – 2,500 markers • Oct 2005 – 4,000 markers Advisory Board Meeting, CSHL 2005

22. The Genetic Map • Recent transfer of knowledge from Jonathan Hodgkin and Richard Durbin is enabling WormBase to update the genetic map when new information becomes available. Advisory Board Meeting, CSHL 2005

23. The end of the CGC contract • Subcontract between CGC and Oxford (Jonathan Hodgkin) runs until May 2007. • WormBase needs to prepare for this. Advisory Board Meeting, CSHL 2005

24. Future Plans • Continue to ensure timely incorporation of all data..including alleles! • Streamline submission processing • Update Web forms • Improve scripts • Improve models Advisory Board Meeting, CSHL 2005

25. Collaborators • The CGC • Jonathan Hodgkin • Bob Herman & Theresa Stiernagle • The Knockout Consortium • Mark Edgley • Jeff Holmes • National BioResource Centre, Japan • Shohei Mitani Advisory Board Meeting, CSHL 2005