WBConfCall 2019.01.03-Agenda and Minutes

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Apologies for absence

Michael P.


New types of Gene Ids

  • Gene Ids of type 'PRJEB28388_chrIII_pilon.g6753' are causing problems for the WS270 run of the gene descriptions pipeline
  • How do we handle these, or can they be ignored?

Meeting Abstracts

  • International meeting abstracts are always included in WB (reliable file format, i.e. easily parsed)
  • Regional and topical meeting abstracts are no longer included as the file formats (and sometimes permissions) are inconsistent and not easily parsed
  • Sometimes users want search access to the regional and topical meeting abstracts and/or want to include them on their Person report pages
  • Possible solutions:
    • Provide a form for upload
      • Would need to check for potential dups
      • Assume that abstracts weren't modified post-submission
      • Possible issues with permissions?
      • Could input more than just regional/topical meetings (e.g. ASCB meeting)
    • Advertise acceptable file format (i.e. international meeting format) and be more proactive about trying to get regional/topical meeting organizers to generate files in this format
    • Other options?
  • What should be included in Textpresso Central?

WB workshops at IWM 2019

  • WormBase workshop:
    • Gene page
    • WB tools-SimpleMine, RNA seq related tools, SoBA, WoBR, Gene set enrichment, etc
    • Community curation-new author first pass form, phenotype submission
    • Parasite talk
    • Alliance update
  • WormMine and JBrowse workshop
  • Micropublication (maybe separate or folded into the WB workshop)


  • Gene IDs issue seems to be resolved
- Hinxton to make code change to remove the problem IDs from the production files.
  • Meeting Abstracts
- Worm board could set a requirement for worm meeting organisers to allow WormBase to use them.

- Work closer with organising groups to get the data in a format that we need.
  As soon as we get a meeting announcement we should contact to try and make things easier.
  Abstract platform provided by WormBase? - Raymond/JC
     Different meetings have different systems that are rolled into the reg and payment process.

- Here is a the GSA file format please supply data in this format

- Some meeting might not care....but the community will buy into this

- Kimberly will work on a proposal for WormBoard and send it round.