PomBase Planning Meeting 8 May 2014

Cambridge - Meeting Room A, Sanger Building

Action item review

  • AI: Monitor UniProt item on tracker, Ensembl (Paul?) will create mapping, Val will check
  • AI: Re user gff query the new file appears to contain LTRs , UTRs and the correct number of CDS, Mark to send file/ close ticket
  • AI: Val circulate list of proposed PIs and other groups for support letters for additional suggestions. Draft letter
  • AI: Val create a list of the Intermine features which will be useful for PomBase users
  • AI: Re gene page revisions to deal with increasing page length Val to a) document b) make mock ups b) ask for community feedback on proposal
  • AI: Problem with Paco's data. Mark to contact Paco/Luis/Ignacio?
  • AI: Val to make curation tool videos for pombelist/FAQ

Outstanding action items carried forward from previous meeting

Multiple alignment related

  • Is it possible to generate alignments on the sequence set selected only>
  • What is used to generate the multiple alignments?
  • In progress as a broader Ensembl item (is this on a traccker?)

Speed (ETA around a month?)

  • A new track loader where data is combined so that loading is quicker. (progess?)

New (and continuing) Agenda items

Update cycle

Mark to explain code modularisation and updating

Basically a follow up from and more recently (last update, ontologies out of synch)

  • There was an identified issue with the loading process which made it too easy to mis-specificy parts of the load.  
  • Mark is reworking the code to avoid this happening in future (progress update) covering
    • Separate feature development from data releases -it should be possible to push out annotation updates rapidly provided the web code and schema are stationary.  Ideally, we would have a separate server where new features are developed independently of the release.  The data release could be automatic, regular (and more frequent);  new features would be tested elsewhere (off a development branch) and merged into the live code when ready, and a new webcode/website release is made over the existing data. 
      • Only make the fix once and reload, don't make a temporary fix
      • Formally documentation of the procedure to be followed in each release which should prevent this from happening in future (and most importantly, ensure that full integration always occurs before release on live).
      • Length of time it takes now to make a release (based on a problem free run). Do we have a current estimate how long each part takes, and how much human intervention is required

Browser Tracks

Track organization and zooming:

Transcriptome tracks (actually a labelling issue)

Comparative view, demo fixes

Hosting high-throughput datasets

Antequera data Last comment Luis wanted to check the modified wig tracks, but I have not heard back so I'll push the release through, but without the tracks live.   If everything is good I can just redeploy the live server once they have been given the all clear from them (current status).

UniProt? mapping

Updating UniProt? mapping periodically (procedure)

Priority Jira tickets

Plan: On that basis of each monthly release cycle; decide at the start of the cycle what we expect to do (in terms of new development or incorporation of data sets) over the course of the cycle, and when it is expect it to be ready; and EBI will keep us informed of any deviations from this plan. On this basis we will identify priorities for V 43


Usage stats

GO annotation propagation over regulation

e.g. mitotic cell cycle + regulation of mitotic cell cycle etc


Phenotype ontology

  • 3200 terms


Other general issues


new ? open ? stalled ? unowned ?

Everyone, please answer queries from the community within a couple of days and follow up as appropriate


Canto annotations (from 2013-??-??)

ItemMarch meetingApril meeting May meeting July 3 Aug 18 Oct ??Nov 20 Jan 20March 1 May 7
All publications975597619773 9935 9989 10025 101201013310294 10356
Un-triaged publications042 1 0 0 0 3 1 32
Curatable publications47354740 4780 4877 4896 4909 4951 4963 5029 5017
Publications with Approved sessions580600 647 674 712 791 884 928 981 1083
Publications with active sessions245247 265 249 246 209 225 228 206 220
Publications with session needing approval144 416 18 35 23 20 8 6
community curatable publications - -- 262 351 385 433 446 454 526
community curated publications with approved sessions- -- 31 58 80 94 110 132 159
curatable publications without sessions----3730?3542 3515 3566 3256


  • Discuss NAR issue paper


  • C-S group data and PombeMine
  • BYG (Antonia)
  • ISB (Midori) phenotype talk, 4 posters (Canto (with GMOD), Matrix, PomBase, FYPO), informal Canto demo (install and use, with GMOD)
  • GO consortium and SAB (Val)

News and Outreach

Next planning meeting


Last modified 6 years ago Last modified on May 8, 2014, 12:28:23 AM