WBConfCall 2015.08.06-Agenda and Minutes
From WormBaseWiki
Contents
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
- 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>
