WBConfCall 2013.10.17-Agenda and Minutes

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WormMine WS239

  • maybe JD can give an overview of the new things
  • Thoughts, reactions?

database URL/URIs

  • where should we store these?
    • acedb + website flat file
    • website flat file only with only database name and description stored in acedb
  • can there be an easier way to update the URL/URIs on the web

ABM 2014

  • when?
  • where?

Release Themes

  • protein folding / pathways WS241
  • ncRNA / specific ncRNAs (lincRNA/snoRNAs) WS242



  • 5.3 days build time, checkpoints used to resume
    • 2d14h for build without sequence generation
    • 2d7h to generate dna sequences from located features
  • sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11
  • richer classes to query (example RNAi, etc.)
  • link to JDs wiki:
  • CDS locations not included in WS239

JD's announcement email:

WormMine WS239 is now up for testing:

Please find the new WormMine build here:

Data changes from WS238:

  • genomic fasta, protein fasta, genes from gff3, transcripts from gff3 has been expanded to represent all species in wormbase (besides any of the "sp" species)
  • the fields of data for each Ace type has been expanded. Wiki has been updated: http://wiki.wormbase.org/index.php/WormMine#Data_contained_in_WormMine
  • RNAi included
  • CDS locations have been temporarily omitted due to them being loaded incorrectly in the last build.

Build released to curators for testing, will be pushed to production once approved.


  • current: flatfile in the github repository (problem: wrong formatted commits)
  • future: potentially an update form/site
  • proposal: remove the URLs from database (to make it clear the repository is the canonical source)
  • proposal: remove the URL_constructor from model


  • early next year
  • Hinxton


  • JSON dumper too slow
  • delay between GeneAce <=> NameDB synch
  • make sure that NameDB <=> GeneAce is synched weekly
  • proposal: do a nightly JSON dump
  • proposal: put the database on the cloud


  • call for letter of support for their new funding cycle

Themed Curation

  • collaborate to curate the protein folding pathways for WS241
    • potentially comparative analysis across species

Curation Focus ideas for themed releases


  • we could add ncRNAs to the other non-cores from other databases (Hinxton) and look through literature (CalTech)