WormBase-Caltech Weekly Calls

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.

February 10, 2011

• Should we have a Caltech project/site manager? We'll look at the issues to be solved first

• Todd would like to know more about what's going on at Caltech
  • What would Todd like to know about? New ideas, data types?
  • What can we communicate more effectively to Todd?

• Should we take minutes of Caltech WormBase group meetings and send around?

• Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on

• Bitbucket use
  • How do we see only what pertains to us, individually?
  • Paul: good way to document bugs and fixes, problems/solutions
  • Bitbucket Wiki - does that capture what people want/need to see?
  • Who should Todd follow? What would Todd like to know about?
  • Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
  • Should we develop best practices guideline for Bitbucket use?
    • Avoid posting topics that are too specific or too vague?
    • What do we want most to get out of Bitbucket?
  • Curation efforts? No

• SAB Meeting
  • Not much feedback for literature curators
  • User interface stuff took precedence
  • Paul: Testing, spot-checking website for errors
  • Web issues, e-mails from Gary and Oliver

• WormBase-wide conference call twice per month
  • First & third Thursday of the month
  • Starting next Thursday (2-17) @ 8:30am PST
  • Web redesign meetings on Thursdays will have to be every other week? Do both same day?

• Raymond: WormBase mirrors
  • Do we want to implement the Genome Browser for the mirror(s)? If practical
  • It seems as though Caltech mirror has been crashing often
  • Has the Caltech mirror been working for people lately? Yes, more or less