WBConfCall 2012.07.019-Agenda and Minutes

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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


  • 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


  • 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


  • 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)


  • 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