WBConfCall 2015.08.06-Agenda and Minutes

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Intermine Status Update (Paulo Nuin and Sibyl)

Slides: http://wiki.wormbase.org/images/WormMine-v2.pdf


  • news items for the release letter
  • new worm: C.elegans (hawaii strain)
  • will be used as reference release for other sites (EG, etc.)

Function vs Mutant

  • Function vs Mutant Phenotype Gene Classes - Submissions to NCBI and EBI
  • see email thread: Function vs. mutant phenotype gene classes
  • categorise the gene classes

WS251 build dates

  • Models freeze, data upload

WormMart End of Service

Now is time to unplug?



slides are here

  • Paolo (Alberta Health Services)
  • runs off AWS
  • total 1 week of building time first time (3/couple days for later attempts after optimisations)
  • ~180 GB
  • currently WS249 / will be updated to WS250 and the new InterMine version for the WS250 release
  • check the test instance, which will be announced at dev or staff before full release
  • decide which data classes to add next (and see if it is in github already as ticket)

WS250 / Hawaii

  • will show up on the Genome Browsers as a Tier III / non-core "species"
  • with mapped gene models from N2, gene models will not necessarily translate
  • currently there is no curation planned

WS251 dates

  • seems fine
    • models 17th of September
    • upload 2nd of October
    • FTP 30th of October
    • staging ~ 1st of December
    • live ~ early January

WormMart End of Service

  • will retire with WS251, as WormMine should be reasonable stable at that point
  • Raymond and Todd will see if they can find a log for archaeological reasons

Gene Class Categories

  • curate protein names?
  • automatic naming based on gene class descriptions?
    • requires gene_class categorisation into functional/phenotypic
    • would need adaptation of the UniProt nomenclature further down the line
  • cooperate with UniProt on curation?
  • we got a list of potentially phenotypic classes which we will use for WS250, but would be good to do "better" for WS251.
  • there has been previous work on it during WS224 (2011) <Karen>