Difference between revisions of "WBConfCall 2018.05.17-Agenda and Minutes"

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**A 'relevant' genotype would be selected at the time of curation, and exported to AGR.
**A 'relevant' genotype would be selected at the time of curation, and exported to AGR.
**The 'absolute' genotype could still be completely captured in WB.
**The 'absolute' genotype could still be completely captured in WB.
**Can we move forward on creating a server/system for creating genotypes in WB?

Revision as of 16:38, 17 May 2018


HelpDesk - Kimberly

Helpdesk Issues Still Open

WBStrain ids

  • would be good to get a list of people who need to be able to create new strains
  • will reside temporary in the old NameServer at Sanger and then move to the new Datomic one on AWS

SAB - Toronto, CA



  • On call: Adam, Cecilia, Chris, Daniela, Juancarlos, Karen, Kimberly, Paulo, Raymond, Scott, Sibyl, Todd, Valerio, Wen, Kevin, Paul D, Gary, Matt, Paul K

HelpDesk - Kimberly

Helpdesk Issues Still Open

  • I am trying to have access to fosmid ...
    • On staging, we will begin providing the end sequences
    • We've never had the full sequence, so if we were providing a "fosmid" sequence, it might have been the intervening genomic sequence
    • What would users want?
    • It seems we could provide the intervening sequence but we need to communicate with users about what they're actually getting, i.e. a prediction.
    • Would this be a potential source of confusion to users, though, who may need to validate the sequence against a clone they order from Don Moerman's group?
    • Resolution: for next release, provide intervening genomic sequence but make it clear that it's predicted from genomic.
    • Chris will check and close the original ticket, if the changes Adam pushed are okay.


  • Bulk assigning strain IDs to existing strains is easy.
  • How do we assign new strain IDs at the point of curation?
  • Will treat similarly to variations, i.e. use a name service to check if an ID already exists; if not, can request a new strain ID to use in postgres curation database.
  • Who needs access to the name server for this?
    • Chris, Daniela, Karen, Ranjana
  • Discussed institutional vs personal sign-on; personal is better, allows for assignment of WBPerson IDs
  • What additional information will be solicited when requesting a new strain ID?
    • Public name is most important
    • Reference?
    • Genotype?
    • This really is an issue of what gets curated where.
    • Ideally, we'd have a central curation database (just saying) that would allow immediate entry of the data.
    • Another option is that all strain information would come from Caltech curation.
    • Would there be anything left for Hinxton to add or do wrt strain curation?
    • One caveat: if author's potentially correct data in the paper when they submit the strain data to the CGC, how would we reconcile that?
    • It would be good to have a shared data model with the CGC, maybe even share the same curation tool.
  • Circling back, do we really need strain IDs?
  • Are strain names unique?
    • Karen has found some strain and clone names that are the same.
  • Todd did some analysis several years ago to see how many classes have overlapping entity names.
    • There were some wrt CDS and transcript; cell and cell group (no longer an issue), but overall the issue was not that bad.
  • For AGR, Sibyl created an ID resolver page. Kevin tested and, so far, hasn't found any issues.
  • There is also the issue of assigning unique IDs to genotypes. Should this issue be coordinated with assigning strain IDs?
  • Raymond: can this change be coordinated with moving to the centralized curation database?
  • Is use of the strain server an efficient way to curate?
    • Would it be possible to create a strain in the OA during curation? Would this be more efficient?
    • Strain IDs could be created during curation, added to postgres, and immediately available for curation, similarly to variation IDs.
    • If there were conflicts with the information in the CGC, we would ask the CGC to correct it, so that the information in WB and the CGC is the same.
  • What's the plan?
    • Check which strain fields are free text vs controlled list in OA
    • Create a strain curation form that would allow curators to create WBStrain IDs and associated information that could be used immediately in the OA.
  • Discussion on creating genotypes in WB
    • What is a 'relevant' genotype? This may depend on the organism.
    • A 'relevant' genotype would be selected at the time of curation, and exported to AGR.
    • The 'absolute' genotype could still be completely captured in WB.
    • Can we move forward on creating a server/system for creating genotypes in WB?