WBConfCall 2012.07.019-Agenda and Minutes

July 19, 2012 COnference Call Meeting Minutes

WormBase 2012 Grant Renewal

• We would like to assemble a first draft of the grant proposal in which we describe an extension of existing activities
• First draft should be assembled by the end of July
• Ultimately, we would like to have the proposal conent be ~1/3 old/existing content & features, ~2/3 new content & features

OICR

• Two topics meetings (Todd and Abby attended)
• Working to address issues raised at those meetings
• Make Tier II & III species more accessible
• Updating GBrowse
• Worked to standardize presentation of data on GBrowse
• Cursory gene pages for Tier II and III genes
• Planning a user survey
• Preparing for grant

Hinxton

• Build for WS233
• Problems with scaling/mapping new variations (600k to 1.5M variations)
• Million mutation project
  • 1.5 million variation objects, ~800,000 from MMP
  • Were being submitted to dbSNP
  • Since these (MMP "SNPs") were synthetic, they have been removed from dbSNP as they were deemed inappropriate
  • WormBase is now the official and sole source of the MMP data
• Long non-coding RNA (lncRNA) submissions
  • Classification: intergenic vs. gene overlapping(?)
• Gary has finished with modENCODE TF binding site data
• Database corruption (ACEDB) problem
  • Thought it was machine problem
  • Reproduced by WashU
  • Brugia data?
• C. elegans sequence errors
  • People sequence their own N2 strain
  • Working to confirm errors using RNA-Seq data and ESTs
  • Good representation of current reference alleles in RNA-Seq data(?)
  • Bob Waterston's group has sequenced several strains, no other N2s in the world have alleles they have
  • Consensus wild type sequence? Probably too difficult to get 'perfect' genome sequence
  • Resequence CGC N2 strain? We would need to do a good job sequencing & assembling the genome; can we use a scaffold?
  • Restrict ourselves to changing things that impact gene models?
• Last week in August, Hinxton will send a DB to WashU, WashU can then edit ~50 gene models before upload (at end of August)?

Cell lineage

• ?Tree and ?Tree_node classes in ACEDB; do people use them?
• Website does not use them
• Cannot accommodate acyclic graphs; thinking about making nodes unique?
• Tested in XACE, is doing OK
• Primary cell lineage file is OBO file (viewed with OBO Edit)
• Ported out into ACEDB for the website

WashU

• John and Phil working on Brugia
• A lot of work to get database and history maker/curation tool working
• Data corruption problems mentioned by Kevin
• Looking over set of genes that were curated as test run by EBI
• Just able to start serious curation this week (with curation tool)
• Tamberlyn working on reducing backlog in BitBucket, C. elegans tickets

CSHL PCR products

• Kevin discovered PCR products from CSHL (CSHace) that didn't get migrated to CITace
• Caltech never got a complete dump from CSHace with comparisons?
• EBI has copy of the CSHACE dump
• Mystery mappings during RNAi mappings
• CSHace has PCR products not in CITace
• Seems to have been an incomplete migration
• Caltech will take CSHace data and integrate into CITace
• Kevin will submit data to Caltech (data and class IDs)

Caltech

• Gene_regulation and YH classes will become obsolete
  • Need to make sure that Gene Regulation display can take information from "Regulatory" subtypes of Interaction objects
  • We can display gene regulation interactions in Interactions widget (in Cytoscape view) AS WELL AS in the Regulation widget
• Molecule & Process pages in the works
• Legacy data for genetics into computer vocabulary for phenotypes
  • over 2500 genes in C. elegans I and II books that have legacy data attached to it

Survey strategy (Todd & Abby)

• Rotating questions/Question of the day on the home page, with a link to a survey
• Need to get data in aggregate to a series of questions
  • Examples: What is your position (undergrad, student, postdoc)? Where are you working? etc...
• Deadline? Run for a month, should get a satisfactory response