Скачать презентацию Worm Base and the CGC Mary Ann Tuli
e6827f2a54d58b5120d115b478928edb.ppt
- Количество слайдов: 25
Скачать презентацию Worm Base and the CGC Mary Ann Tuli
Скачать презентацию Worm Base and the CGC Mary Ann Tuli
Worm. Base 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 (WS 124) ≈ 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 CGC E-mail Geneace Curator Submitter Web Form Mary Ann Tuli Advisory Board Meeting, CSHL 2005
Developments – Tracking gene names Before: Gene_name: Other_name: abu-1 pqn-1 Gene_class: abu-1 Remark“pqn-1 is Other_name of abu-1 and has been merged into it” abu-1 pqn-1 Gene_class: Old_member: After: Gene_name: Other_name: Gene_name: pqn-1 Former_member_of: pqn Mary Ann Tuli Advisory Board Meeting, CSHL 2005 pqn-1
Developments – Tracking gene names ≈ Former_member_of and Old_member introduced in WS 144 ≈ WS 150 = 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 (WS 144) ≈ Live, Dead or Suppressed Mary Ann Tuli Advisory Board Meeting, CSHL 2005
The Variation Class Locus Class Allele Class Variation Class WS 140 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 E-mail NBP Geneace Curator Submitter Web Form 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 Worm. Base 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 R 09 B 3. 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 Worm. Base 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 2007. ≈ Worm. Base 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 Bio. Resource Centre, Japan ≈ Shohei Mitani Mary Ann Tuli Advisory Board Meeting, CSHL 2005
Скачать презентацию Worm Base and the CGC Mary Ann Tuli
e6827f2a54d58b5120d115b478928edb.ppt