WBConfCall 2015.10.15-Agenda and Minutes

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  • We need to update the release schedule nb it's over Xmas and SAB

Pristionchus gene names

  • The issue is: Pristionchus gene names/assembly in the research community drifting away from those in WormBase
    • Papers being published with Wormbase-style gene names that have not been approved by WormBase (e.g. WBPaper00048552)
    • These are linked to anonymous annotations on pristionchus.org that cannot be cross-referenced back to WormBase
    • Communication / Data flow between pristionchus.org and WormBase could be better. Conversations started.
  • Is there a similar problem with other non-elegans/parasitic species?



  • WS251 release scheduled 1st January
  • WS252 freeze date start of December - Dec 4 (Dec 1 local Caltech upload)
  • Build will finish at start of January
  • Live on WormBase start of March
  • SAB would fall in middle of staging/webdev part of cycle
  • Upload after Thanksgiving holiday

Pristionchus gene names

  • Ralf Sommer has been emailed (awaiting response)
  • WormBase has two ways of handling a genome: ownership or importing the data from someone else
  • Pristionchus is currently a mixture of these
  • Proposed that we should take one direction or the other
  • Current gene models in WormBase are >5 years old
  • Data in GenBank is 7 years old
  • Also a third copy of genome on Pristionchus.org

Help tickets pending


  • Web team to look at


  • Pointing users to the FTP site
  • Downloads are not archived
  • Will be resolved in WormMine
  • Discussion about user documentation:
    • Should there be a widget specific user guide?
    • Can link from widdget to a static page or wiki page.
    • Not sure if all documentation should be rewritten at the present time.

#4264 WormBook nomenclature chapter

  • Rather than including species prefixes in chapter, it would be ideal to point to a page on WormBase
  • Cannot generate a URL to a specific widget in website
  • Discussion about website being a good place to store documentation:
    • MediaWiki is easier to embed into websites
    • Wikis do not have stable URLs as the document name can be changed
    • Wikis (or similar) are generally the easiest for people to edit
    • Can protect document names to keep URL stable
    • Opportunity to address problem of documentation distribution
    • Todd to compile a shortlist of possible solutions and send around the group for everyone to look at
  • Current list should go on WormBase wiki and linked to from current WormBase page
  • Deprecated nomenclature page already presrnt on the wiki, this can be updated with the latest text

#4278 Links with variation

  • Web team will look at next week