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

Advisory Board Meeting, CSHL 2005 Growth of genetic data

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 WBGene ≈ ?Gene model introduced in April 2004 (WS124) ≈ Name server – streamlining gene tracking

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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 CGC Gene Names

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Gene Naming Pipeline Web Form Submitter Geneace Curator CGC

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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Developments – Tracking gene names ≈ Former_member_of and Old_member introduced in WS144 ≈ WS150 = 663 CGC Other_names in 291 gene classes

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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Developments - Status ≈ After: ≈Status tag introduced in Gene and Variation model (WS144) ≈Live, Dead or Suppressed

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 The Variation Class Variation Class WS140 Locus ClassAllele Class

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 The Variation Class ≈ Type of Variation ≈Deletion ≈Insertion_and_deletion ≈Insertion ≈Substitution ≈Mos_insertion ≈Transposon_insertion ≈SNPs

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Allele Submission Pipeline Web Form Submitter NBP Geneace Curator

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Knockout Alleles ≈ Mark Edgley ≈ Jeff Holmes

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Knockout Alleles ≈ Shohei Mitani NBP

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Strain Data ≈ Sent periodically to WormBase from Theresa Stiernagle ≈ Leads to merges of Gene names and sequences ≈ Leads to updates of tag- genes

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 Laboratory Data ≈ Laboratory data sent from the CGC and Caltech

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 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

Mary Ann Tuli Advisory Board Meeting, CSHL 2005 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.

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

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

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