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


December 17th 2012

Outstanding Action items from Nov 9th

  • Action: Curators look into acquiring data from strain collection in Japan (Not done)
  • Action: PK et al. to create Jira tracker for Ensembl genome browser issues; PK to triage tickets
  • Action: Diagnose the cause of the not synching of the update (Mark) (OK)
    • AI Val will provide the feedback from the fission yeast community on the browser to Giulietta (DONE, have response to go through)

New Action items from Nov 4th

  • AI curators look at vertebrate demo of vertebrate browser (beta)
  • AI Showcase community curated papers on front page (check that the community curated flag is loaded into Chado)
  • AI remove left hand menu from front page
  • AI val/curators to mock up rearranged front page (look @ other MODS , I quite like SGD's, we should have a "fast track" your paper link like Flybase, but this would take you to the curation tool)
  • AI next meeting demo of curation tool
  • AI Val will announce next stage of community curation and request people eager to participate contact us.
  • AI Val/curators will start to send out a large number of community curation sessions
  • AI Curators will concentrate on older presumably quicker papers, or any papers which are unlikely to get curated (retired labs etc)
  • AI send some papers to Paul to curate
  • AI Next priorities for Mark i) check that between EG release data reload works from beginning to end
  • AI Mark jira items required for GeneDB commissioning (only 11 remaining)
  • AI Mark add a new jira component for hosting new datasets
  • AI Next month discuss next priorities
  • AI Val to enquire about "stand" at PomBase meeting
  • AI Organise a large general "PomBase" banner
  • AI Sam's data, decided to add "condition" Val will contact Sam, also need to add PMID and chase "quiescence term", then decide where this data should live (pombase-embl)?
  • AI Next meeting doodle poll 1-17 Dec (done, obviously)
  • Gene names and products will be loaded from Chado
  • AI discussion about displaying interactions in both directions


  • website front page
    • Look at all proposals/ mockups, come up with a plan
      • Content
      • overall format separate sections, or single rolling (possible new feature/ data updates etc)
      • specific format, font/ colours/spacing
      • images,
        • rotating?/ random?
        • collection of images how? /jurg has supplied some are they suitable?, where should these live?
        • citing source, include in figure?
      • Highlighting community curation ? which method
      • events
      • "fast track" your paper link like flybase
      • help and e-mail icons
      • menu bar
  • EMBL submission file

Updates from various Areas

Curation Update

  • All papers are triaged (upto ~)
  • *update* Of 9511 papers 4604 are "curatable" with gene product specific information (no change)
  • 6297 annotations in curation tool
  • 682 curation session (papers) in progress (previous 613)
  • 432 ? approved (previous 338)
  • 9 needing approval (previous 47)
  • Intend to start sending our more papers to community once phenotype annotation visible in PomBase (done) also need some changes to the curation session management (who paper was sent to and who eventually curated)

Phenotype Ontology (Midori)

  • 1795 phenotype terms
  • ordinary incremental progress

Chado loading (Kim)

  • Anything to report ?

Curation tool (Kim)

  • Anything to report ?

Review (Mark)

  • Go through jira tracker items to decide priorities

Current jira status: Open 162 Closed/Resolved? 908 (was 163/868 last meeting, Nov)

Next priorities (Pombase website)

  1. Host new dataset NG30
  1. GeneDB decommissioning tasks

  1. Post GeneDB decommissioning tasks These are features which are provided by GeneDB, and used, but are not as critical. Provided they are replaced fairly quickly people can probably survive for a while if the old site is taken down
  1. Hosting genome wide datasets
  1. Unscheduled items *

Problems reported

Meetings Attended/ Upcoming

  • proposed Workshop for 2013 (International meeting) straw poll?
  • Proposed PomBase 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree


  • Next meeting (doodle)

PI's meeting