Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
== May 13, 2021 ==
 
  
=== Textpresso supplement ===
+
== June 3, 2021 ==
* Due Monday
 
* Michael working with Paul S
 
  
=== AWS credits ===
+
=== Reserving meeting rooms ===
* Michael and Valerio were awarded AWS credits, more than they can use
+
* Raymond encountering challenges with setting up regular meeting room reservations in Chen building
* Maybe they can be repurposed
+
* We've been asked to make reservations one week in advance
* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
+
* Need to use a room if we reserve it
  
=== Automated gene descriptions ===
+
=== Summer student(s) ===
* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
+
* Anatomy function project with Raymond
* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
+
* Many types of anatomy function data submitted via AFP
* May be the focus of an Alliance supplement
 
* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
 
  
=== IWM 2021 WB Workshop ===
+
== June 10, 2021 ==
* Scheduled for June 22, 2021
+
 
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
+
=== Variation-Gene Associations ===
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
+
*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
* Here is the submitted workshop schedule:
+
*https://github.com/WormBase/author-first-pass/issues/204
  11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
+
*https://github.com/WormBase/website/issues/8262
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
+
*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
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
+
 
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
+
===Variation in name service but not in OA===
  12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
+
*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

Latest revision as of 18:59, 10 June 2021

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June 3, 2021

Reserving meeting rooms

  • 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)

  • Anatomy function project with Raymond
  • Many types of anatomy function data submitted via AFP

June 10, 2021

Variation-Gene Associations

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