Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
  
 +
== June 3, 2021 ==
  
== May 7, 2020 ==
+
=== 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
  
=== Alliance COVID Page ===
+
=== Summer student(s) ===
* Available on stage
+
* Anatomy function project with Raymond
* Textpresso for Coronavirus up for testing
+
* Many types of anatomy function data submitted via AFP
  
=== SimpleMine at Alliance ===
+
== June 10, 2021 ==
* Still some confusion about what it is
 
* Will try to help clarify on PI meeting on Friday
 
  
=== Development environment for Alliance work ===
+
=== Variation-Gene Associations ===
* Raymond and Juancarlos have been working on
+
*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
* Existing hardware is strained; set up virtual machine
+
*https://github.com/WormBase/author-first-pass/issues/204
* Still some technical issues
+
*https://github.com/WormBase/website/issues/8262
 +
*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
  
=== Open Publishing Festival ===
+
===Variation in name service but not in OA===
* Later this month
+
*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?
* Micropublications involved
+
*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 ?)
* Organized by the Collaborative Knowledge Foundation
 
* Will involve publishers of books, journals, etc.
 
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 
* Open to all
 
  
=== Genotype class ===
+
*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:
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
 
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 
* Would be good to be clear/transparent about which components were automatically inferred
 
  
=== WS277/278 ===
+
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
* Pipelines are pushed back by about 14 days/2 weeks
 
  
 +
making sure to enter the variation with name-space-WBVarID like:
  
==May 13, 2020==
+
gk315316 WBVar01148785
  
=== SURF students ===
+
and then, after refresh, it should be available to the OA. Hinxton never has to get involved in this scenario.
* Welcome Fernando!
 
* Will work on neuron function with respect to dauer formation
 
  
=== Progress Report ===
+
=== Confirm WS282 Upload Dates ===
* Review Google Doc from Paul to make sure you're latest updates are there
+
*July 6th?
* Doc here:
+
*Data freeze/upload date on the release schedule is July 12th
  
===Genotype class===
+
=== CenGen bar plots ===
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
+
*Initially discussed to have the bar plot images going in as image data
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
+
*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.  
*Disease OA annotations now converted to the newly created genotypes where needed
+
*They can provide the underlying data and have the WB team generate interactive plots for each gene
*Need to work on disease dumper changes next
+
*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
  
=== What genes should be linked to genotypes? ===
+
* Bring in data  both as pictures and interactive bar plots
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
+
* Ping Hinxon on GitHub to move this forward
* What should we consider a "relevant gene"?
 
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
 
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
 
* For rearrangements, consider relevant any genes "inside" the rearrangement?
 
 
 
=== Volunteer Community Curators ===
 
* Have had an additional 13 people volunteer
 
* Single one-on-one tutorial for someone in Hong Kong this past Monday
 
* Chris will hold a tutorial today and tomorrow for everyone else
 
* Have received many new community annotations from volunteers (and authors), validation still pending
 

Latest revision as of 18:59, 10 June 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May


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