Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
== June 3, 2021 ==
 
  
=== Reserving meeting rooms ===
+
== July 1, 2021 ==
* Raymond encountering challenges with setting up regular meeting room reservations in Chen building
 
* We've been asked to make reservations one week in advance
 
* Need to use a room if we reserve it
 
  
=== Summer student(s) ===
+
=== Importing genes for tm alleles from GeneACE ===
* Anatomy function project with Raymond
+
* https://github.com/WormBase/website/issues/8262
* Many types of anatomy function data submitted via AFP
+
* Nightly dump currently excludes tm allele genes
 +
* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
 +
* Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
 +
* ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
 +
* Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
  
== June 10, 2021 ==
+
=== Citace upload ===
 +
* Curators upload files to Spica for citace upload on Tuesday (July 6)
  
=== Variation-Gene Associations ===
+
=== Chen B1 kitchen Usage Considerations ===
*Some QC on AFP-extracted data led to the realization that at least some of the 'tm' variations aren't associated with genes on tazendra
+
* Clean up after oneself.
*https://github.com/WormBase/author-first-pass/issues/204
+
* Mark food storage with name and date.
*https://github.com/WormBase/website/issues/8262
+
* Mark storage drawers
*It looks like non-manually asserted variation-gene associations will be generated via the VEP pipeline during the build, so Caltech would need to get this information from each WB release
+
* Consumables
 
 
===Variation in name service but not in OA===
 
*Ranjana: I could not find gk315316 in the OA though it exists in the name server. I agree that we probably don’t want to let all the million mutations into the OA since that would slow the drop-downs, but when we need one for curation, what needs to be done?
 
*Juancarlos: That might be right.  It seems to try to create the variation in the name service, and if it gets a 409 Conflict error, it adds it to the temp variation file, and the obo_ tables in postgres. Since it fails to create in the name service, that's probably okay with Hinxton, and since it gets added to postgres, you should be able to use it in the OA, and since it gets added to the temp variation file, on future updates of the ontology it gets added again. Probably best if someone confirms that's the process (and maybe points us to a wiki ?)
 
 
 
*Solution from Karen and Chris: If the Hinxton name server already has the variation but it isn't in the OA (as expected for Million Mutation Project variants like gk315316), we just need to add it through the old temp variations CGI:
 
 
 
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
 
 
 
making sure to enter the variation with name-space-WBVarID like:
 
 
 
gk315316 WBVar01148785
 
 
 
and then, after refresh, it should be available to the OA. Hinxton never has to get involved in this scenario.
 
 
 
=== Confirm WS282 Upload Dates ===
 
*July 6th?
 
*Data freeze/upload date on the release schedule is July 12th
 
 
 
=== CenGen bar plots ===
 
*Initially discussed to have the bar plot images going in as image data
 
*CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.  
 
*They can provide the underlying data and have the WB team generate interactive plots for each gene
 
*Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
 
*The first approach may be more work but better in the long run as we store the data
 
*Will ping Hinxton and see how they can integrate the data
 
 
 
* Bring in data  both as pictures and interactive bar plots
 
* Ping Hinxon on GitHub to move this forward
 

Revision as of 16:49, 1 July 2021

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July 1, 2021

Importing genes for tm alleles from GeneACE

  • https://github.com/WormBase/website/issues/8262
  • Nightly dump currently excludes tm allele genes
  • Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
  • Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
  • ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
  • Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?

Citace upload

  • Curators upload files to Spica for citace upload on Tuesday (July 6)

Chen B1 kitchen Usage Considerations

  • Clean up after oneself.
  • Mark food storage with name and date.
  • Mark storage drawers
  • Consumables