WBConfCall 2016.10.06-Agenda and Minutes

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WormBook chapters

ticket #5092 with reference to #5080 https://github.com/WormBase/website/issues/5092

  • Discussion on making available on WormBase the chapters we wrote for the WormBook.
  • There are 11 chapters so far -anatomy, genomic data, gene expression, phenotype, GO, Human disease, intermine, nomenclature, Process&Pathway, website, sequence homology.
  • They could serve as a User guide and are up-to-date. Would be good to have them published. Better to have them on WormBook? Status?


  • models deadline, upload dates etc.

AGR working group updates/action items

  • Orthology
    • Panther data in WormMine
      • Orthology data in WormMine seems *not* to come from WormBase / AceDB
      • Need clarification on (a) what version of Panther was loaded, and (b) how it was loaded
    • Desired update frequency
      • Proposal is to update orthologs once per year. Are we happy with that?
      • Should we adjust our update cycle to accommodate this?
  • Use case
  • Disease-phenotype
    • We will need to produce a data file that has all of the disease data since disease data is not available from WormMine

2017 Worm Meeting

  • Workshop proposals deadline: 15th November 2016


WormBook chapters

  • Proposal : put chapters up on site now, at the same time trying to get them into WormBook (before it closes down)
  • Questions:
    • How to deal with updates?
      • Micropublications a possible model for citable paragraph updates
    • How should we manage the website versions of the articles?
      • Wiki? Perhaps too difficult to maintain consistent format
      • Readthedocs? Content Management System? Web-team to think about this and send round some ideas
    • Lots of other discussion around this topic

WormBase 257

  • Models freeze - 7th October
  • Upload - 27th October

AGR working group updates

  • Orthology
    • Established that Panther data in WormMine came directly from Pather (via InterMine loader), rather than AceDB
    • TH to supply date/version of Panther that was loaded
  • Use-case
    • In basic search, genes will link back to MODs
    • Group now working on more refined use-cases beyond basic search
  • Disease
    • Disease data missing from Mines, so needs to be loaded into AGR via some other means
    • Disease Association GAF files? These do not contain the textual curator-written descriptions
    • Discussion needed with working group on data exchange mechanisms
  • Wednesday curator calls
    • Curator calls will now include an update from each working group
    • Open to suggestions for next topics