wiki:PomBasePlanningMeetingMinutes20130121

PomBase? Planning Meeting Monday 21 January 2013 - Minutes


Monday 21 January, 10:00, Cambridge

Present: Val, Midori, Antonia, Paul, Steve
Remote: Jürg, Dan, Mark
Chair: Val
Minutes: Val/Antonia?

Review of action items from Nov outstanding/Dec

Carried forward Nov

  • 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 (postponed until new session management and documenation is in place. Will continue to send out small numbers of papers)

Carried forward Dec

None - all done, or on jira tracker, in progress

New Agenda Items

  • speed and page loading, all agreed was much too slow AI: Mark will look into why pages are loading slowly / what can be done to speed it up (highest priority task)
  • wild card searching "Not being able to search on partial gene names or IDs" There is no good solution to this problem at the moment. It makes a massively bigger search space (Paul). Could we just search pombe systematic ID’s? (Midori) AI: Mark (?) To look into whether a smaller search space can be searched
  • Scheduled date for when datasets will go live.

We should have a scheduled date for when whatever data set is available will be the next one loaded (Paul). Usually this happens 6 weeks before release (Dan). This only addresses Ensembl genome (Val). Are we loading interim versions? AI Kim: flag the datasets that should be loaded. Mark should load the most recent one of the ones that have been flagged as ‘loadable’.

  • Turnaround time of > 2 months is too long once community curation is launched (version 30 is from 12 November). We should talk about ways to improve this (most MODs update nightly). Mark has worked about doing loads independently. If this can be automated it will be a lot quicker (Paul). We also need to know for when the ‘final versions’ need to be available (Midori).

AI: Mark get an automated pipeline in to do updates quickly. This will allow a more frequent release cycle.

  • implement the RNA/protein expression data from Sam's paper
    • AI Antonia to sort data out (add column for conditions and PMID), and similar date from other groups
      • need an ontology term for quiescence
        • AI add a PBO term (note: was assigned to me in previous draft of minutes, but I don't have direct write access to PBO; Mark generates it from things in chado. I'll look into where it can go. -Midori)
  • Gene name synching (e.g. why is mre11 still called rad32…was changed in early November?)
  • What do we need to tell CRUK lab heads to resolve their firewall problem ?
    • Mark needs to know if their firewall is stripping cookies from pages.
    • AI Val to ask them if this is happening.

Other

AI: Mark to liase with Giulietta to help with making a Pombe community curation video.

Summary of New Action items

  • AI: Mark will look into why pages are loading slowly / what can be done to speed it up (highest priority task)
  • AI: Mark To look into whether a smaller search space can be searched on simple search
  • AI: Kim flag the Chado releases that he and curators agree are ready to load. Mark should load the most recent one of the ones that have been flagged as ‘loadable’.
  • AI: Mark get an automated pipeline in to do PomBase updates quickly. Make planned release schedule available to all PomBase team (especially curators)
  • AI: Mark to liaise with Giulietta to help with making a Pombe community curation video.
  • AI: Antonia to sort cell data out (add column for conditions and PMID), and similar date from other groups
  • AI: add PBO term for quiescence (Midori to draft name & def; Mark to add to PBO)
  • AI: Val to ask CRUK if their firewall is stripping cookies from pages and let Mark know

Meetings Attended/ Upcoming

  • 28 Feb-1 March GO cell cycle ontology contant meeting (GO and Jacky Hayles)
  • March 20-22 BYG 2 posters submitted: Antonia (community curation), Midori (phenotype ontology)
  • April 7-10 ISB, 4 posters submitted: Val (Annotation QC, general PomBase), Antonia (community curation), Midori (phenotype ontology) Mark might want to attend, at least poster sessions?
  • April 10-13 GO meeting is immediately after this meeting. Mark should attend the software sessions

  • Pombe meeting, still need to decide what to do about PomBase/GO/curation demo
    • Community curation walk through (quick but so that people know about it) early on in the meeting. This will allow people to come to the stand and ask questions. We need a longer slot to demonstrate the website (ideally a 30 min slot) but this can be done later whenever tools and resources session is.

Last modified 8 years ago Last modified on Jan 23, 2013, 9:17:36 AM