WormBase-Caltech Weekly Calls 2009

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June 11, 2009

  • Discussion of allele-paper connections
    • Jolene has a Textpresso-based pipeline for identifying alleles in papers
    • Alleles get associated with a paper if there is phenotypic or molecular data
    • List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
  • Discussion of gene-paper connections
    • What criteria should be used for associating genes with papers?
    • Currently being associated manually by a curator during first-pass
    • Could Textpresso be harnessed for this task?
    • There are different evidences attached to gene-paper connections
    • Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
    • Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
  • Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
    • Data type curator could help design a useful query
  • Other gene-object connections
    • Develop a canned query for all objects that should be associated with the gene page
  • Worm Meeting
    • Pre-meeting - meeting rooms?
    • Pre-meeting - practice talks for WormBase workshop
    • Storage for swag - pavillion should be okay

June 18, 2009

  • Worm Meeting and Pre-Meeting
    • WormBase Help Desk Schedule - set for worm meeting
    • Wen may need help carrying boxes of swag
    • Do any Sanger or WashU people need rides to UCLA?
    • Mary Alvarez is working on finding rooms for the pre-meeting
    • Be prepared to report on curation status of your data type and what we might need
  • Author contact information on first-pass form
    • email goes to the first email address found by Textpresso
    • Raymond - we do care where this data comes from
    • Erich - can we send it to the designated corresponding author
    • first-pass curation could capture the corresponding author
    • if the email didn't go to the corresponding author, it may affect our response rate
    • two-stage approach proposal
      • respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
      • going forward, how best to determine corresponding author?
      • keep track of IP address from which the data was sent?
      • add text to email saying that authors may include their contact information in the comments box, if they wish
      • Raymond will proof-read papers to check on corresponding author designation and email addresses
  • Zfin visit - PATO progress, worth looking at
    • Erich noted no genome browser - what is the issue?
    • Their experience with getting figures from journals might be helpful.