WormBase-Caltech Weekly Calls 2009

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.