Version 2 (modified by val_wood, 9 years ago) (diff)


Planning Meeting Tuesday 17 Dec 2012 - Minutes

Agenda for this meeting

Tuesday 17 Dec, 10:00, EBI

Present: Val, Midori, Mark, Dan, Paul
Remote: Kim, Jürg
Chair: Val
Minutes: Mark

Usage stats

Previous Action Items To Carry Forward

  • Action: Curators look into acquiring data from strain collection in Japan (Now moved to Curation tracker)
  • AI Organise a large general "PomBase" banner
  • Demo of curation tool (postponed)
  • Send papers to Paul K.
  • AI Val/curators will start to send out a large number of community curation sessions
  • 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 (decided Kims ftp directory or pombase-embl)


  • Val to continue providing Browser feedback to Gulietta AI VAL chase up pombe community as have not responded to recent requests
  • Discussion about synching of gene names and GO term names when chado version is updated. AI Mark takes some time to consider the order of the loading
  • Finish the final items for the decommissioning of the GeneDB site. AI Val to chase up motif search code from Sanger
  • Discussion about new home page AI open new jira item with mock up
  • Discussion about EMBL submission file

  • Organisation for Pombe2013 Jurg suggested that PomBase? funded the poster refreshments and would get a stand and a talk slot to promote community curation Val suggested trying to get WT small meeting funding for this (on behalf of PomBase?) AI Look into this and forward details to Jurg
    • Stand (£2000)
      • Banners
      • Posters
      • ?Freebees?
    • ?Poster Drinks? - Potential funding

Curation update

Curators have targeted older publications and increased curation volume (papers) from 338-432

Jira tracker update =

  • The rest of the meeting was devoted mainly to the Jira update, prioritising task for GeneDB decommissioning, V 31,32,33
    • AI Val/Midori? to look into where UTR.fasta data came from

New Action Items

  • Redesign of the PomBase front page.
    • VW: Source some images of cells that could be used.
    • VW: Highlight specific papers to display on the front page
    • MM: Convert to a multi-column format.
  • MM: Load the transcriptome datasets listed on JIRA
  • MM: Update xref names before running the update annotation scripts.
  • PK/DS/MM: EMBL submission files. Work out what is going to happen with these going forward (for this Val will first test how close the current file is )
  • Search:
    • MM: Auto-regenerate the search indexes and get ES to set up a new domain and index the PomBase dumps.
    • MM: Get the simple search to include the orthologues.
    • All curators: discussion to nail down what search options and behaviour we really want, then update Jira
  • KR: Generate v31 Chado dump
  • DS/MM: GFF and GTF usage standardisation in ensembl for downloads. Needs assigning.
  • KR: Work on the Session Management for the curation tool.


  • Future meetings to review what data there is available and to discuss what to load.
  • Next Meeting: 21st Jan 2013