Version 1 (modified by val_wood, 9 years ago) (diff)


March 18 2013 6 p.m. UCL London

Present: Steve, Jurg, Val, Midori, Dan, Mark, Antonia

Apologies: Kim, Paul

Action items carried forward and not addressed yet

  • AI Organise a large general "PomBase" banner
  • Demo of curation tool (postponed)
  • AI Val/curators will start to send out a large number of community curation sessions (postponed until new session management and documentation is in place. Will continue to send out small numbers of papers)
  • AI: Mark to liaise with Giulietta to help with making a Pombe community curation video.
  • AI: Val to ask CRUK if their firewall is stripping cookies from pages and let Mark know

New Action Items

  • AI Val will contact Paul K about EBI site wide search indexing PomBase?
  • AI Val will check when Sanger will decommission GeneDB
    • If this is a while we will re look into NCBI updating links, but Sanger will implement forwarding so possibly not necessary

Speed issues

  • Page loading on www is now
    • 1-2 seconds for short pages,
    • 4-5 seconds for long pages
  • Midori mentioned that dev is faster
  • Overall we are generally happy with the speed for now and Mark can move on to the other priority tasks

Regularity of updates

  • Mark will take release on 1st Monday of the Month and then go for release on the third Monday. This allows two weeks for the updates and then do the release on a Monday rather than a Friday
  • Automated pipeline: AI Mark is working on this now with regression testing. Plan is to have a pipeline ready for the next meeting.
    • this will include generation of files for download

Misc items

  • Progress implementing the RNA/protein expression data from Sam's paper AI now tabled for V 34, Kim need to load into Chado and Mark to get display on gene page sorted

  • Missing data
    • AI possibility that some phenotype data is missing, not just conditions, val will look into this

  • Problem with GO slim
    • AI Val will have a look and pinpoint some example missing genes from lists
    • AI Mark will tell us when the ontology data is up to date
  • File format for cDNA
    • AI get rid of :pep (in a parse step)
    • AI Val, find out why Chado uses :pep notation
    • AI Midori put in jira descritpion what cDNA fasta file formats we require

Curation Update

Review of curation progress (See agenda for details) and Antonia's graph showing 5 fold increase in curations per paper since 1980's (excluding HTP)

  • AI Mark will do general PomBase? poster for Pombe 2013
  • AI Midori Look into beer mugs and T-shirts (VW sigh, if I really have to...)

Chado loading / curation tool

  • nothing reported this meeting