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 | + | * 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 [https://github.com/WormBase/website/labels/Intermine 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 as a Tier III / non-core "species" | * 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 == | ||
| Line 43: | Line 46: | ||
==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 == | ||
| Line 52: | Line 56: | ||
* cooperate with UniProt on curation? | * 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. | * 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 | + | * there has been previous work on it during WS224 (2011) <Karen> |
Latest revision as of 17:10, 6 August 2015
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>
