Difference between revisions of "WBConfCall 2015.08.06-Agenda and Minutes"

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=Minutes=
 
=Minutes=
 
== Intermine ==
 
== Intermine ==
 +
[http://wiki.wormbase.org/images/WormMine-v2.pdf slides are here]
 +
 
* Paolo (Alberta Health Services)
 
* Paolo (Alberta Health Services)
 
* runs off AWS
 
* runs off AWS
 
* total 1 week of building time first time (3/couple days for later attempts after optimisations)
 
* total 1 week of building time first time (3/couple days for later attempts after optimisations)
 
* ~180 GB
 
* ~180 GB
* currently WS249 / will be updated to WS250 and the new intermine version for the WS250 release
+
* currently WS249 / will be updated to WS250 and the new InterMine version for the WS250 release
* check the test instance
+
* 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)
+
* decide which data classes to add next (and see if it is in [https://github.com/WormBase/website/labels/Intermine github already as ticket])
  
 
== WS250 / Hawaii ==
 
== WS250 / Hawaii ==
* will show up on the Genome Browsers
+
* will show up on the Genome Browsers as a Tier III / non-core "species"
* with mapped gene models from N2
+
* with mapped gene models from N2, gene models will not necessarily translate
 +
* currently there is no curation planned
  
 
== WS251 dates ==
 
== WS251 dates ==
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==WormMart End of Service==
 
==WormMart End of Service==
* will retire with WS251
+
* 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 ==
 
== Gene Class Categories ==
 
* curate protein names?
 
* curate protein names?
 
* automatic naming based on gene class descriptions?
 
* automatic naming based on gene class descriptions?
** requires gene_class categorisation
+
** 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>

Latest revision as of 17:10, 6 August 2015

Agenda

Intermine Status Update (Paulo Nuin and Sibyl)

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

WS250

  • 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?

Minutes

Intermine

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>