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 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
=== Reserving meeting rooms ===
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* 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 ==
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== September 2, 2021 ==
  
=== Variation-Gene Associations ===
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
*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
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Needed for
*https://github.com/WormBase/author-first-pass/issues/204
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*AFP community curation
*https://github.com/WormBase/website/issues/8262
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*microPublication author tracking for all species
*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
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
===Variation in name service but not in OA===
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Problems:
*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?
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*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
*Juancarlos:
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*need to do this outside of Alliance
**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
+
Action
us to a wiki ?)
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*Paul talks to zfin about interest in person pages
 +
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 +
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
=== Confirm WS282 Upload Dates ===
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Will do
*July 6th?
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*create biolink model based on current WB postgres/Caltech model
*Data freeze/upload date on the release schedule is July 12th
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*Adam will add tables when we have them
  
=== CenGen bar plots ===
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2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
*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.
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== September 16, 2021 ==
*They can provide the underlying data and have the WB team generate interactive plots for each gene
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*Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
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1. CeNGEN enriched genes per cell type data targeted for WS283.
*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
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2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
 +
 
 +
== September 23, 2021 ==
 +
 
 +
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
 +
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
 +
* Update the WB page on citing WormBase
 +
 
 +
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 2021

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September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.