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]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
== February 6, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
=== Worcester Area Worm Meeting talk ===
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
* Confirmed for December 2020 or February 2021
 
  
=== Alaska software ===
 
* Code developed and maintained by Joseph, but not long term solution
 
* Raymond and Eduardo talked about taking it over
 
* Why have a web application vs. a command-line application?
 
** Wanted to make it easy, but also to capture meta data for WB
 
* Should/will find out from Joseph about how hard it is to maintain the software
 
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 
* Array Express tried requiring more structured meta data, but authors stopped submitting
 
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
 
  
 +
== June 3, 2021 ==
  
== February 13, 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 Literature Group ===
+
=== Summer student(s) ===
* Held first meeting on Monday, February 10th
+
* Anatomy function project with Raymond
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
+
* Many types of anatomy function data submitted via AFP
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
 
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
 
  
=== ?Genotype class model ===
+
== June 10, 2021 ==
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
 
* Can aim to implement for WS277 but may have to wait until WS278
 
  
=== Genotype OA ===
+
=== Variation-Gene Associations ===
* Will put documentation [[Genotype|here]]
+
*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
 +
*https://github.com/WormBase/author-first-pass/issues/204
 +
*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
  
=== WB All-Hands Meeting ===
+
===Variation in name service but not in OA===
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
+
*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?
* Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
+
*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:
  
== February 20, 2020 ==
+
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
  
=== Genotype ===
+
making sure to enter the variation with name-space-WBVarID like:
* We will equate superficially similar/identical genotypes for now
 
* What if labs sequence strains later and find out more?
 
* Labs will have to report strains and their sequence and we back-curate accordingly
 
  
=== VC2010 assembly genes ===
+
gk315316 WBVar01148785
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
 
* How to best handle these "extra" genes?
 
* We could make different species entries that specify the assembly version
 
  
 +
and then, after refresh, it should be available to the OA. Hinxton never has to get involved in this scenario.
  
== February 27, 2020 ==
+
=== Confirm WS282 Upload Dates ===
 +
*July 6th?
 +
*Data freeze/upload date on the release schedule is July 12th
  
=== WB Project meeting ===
+
=== CenGen bar plots ===
* Early May (~May 7th, 8th)
+
*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
  
=== Genotype ===
+
* Bring in data  both as pictures and interactive bar plots
* [[Genotype|Genotype Wiki page]] updated
+
* Ping Hinxon on GitHub to move this forward
* Will start building Genotype OA
 
 
 
=== Outreach inbox ===
 
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
 
* Many are bounced emails messages
 
* Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
 

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