Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(375 intermediate revisions by 9 users not shown)
Line 21: Line 21:
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
== June 3, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
=== Summer student(s) ===
 +
* Anatomy function project with Raymond
 +
* Many types of anatomy function data submitted via AFP
  
 +
== June 10, 2021 ==
  
==August 6th, 2020==
+
=== Variation-Gene Associations ===
 +
*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
  
===Experimental conditions data flow into Alliance===
+
===Variation in name service but not in OA===
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
+
*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?
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
+
*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 ?)
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
 
*So for data flow into Alliance:
 
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
 
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
 
* How do we handle genetic sex? Part of condition?
 
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
 
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
 
  
 +
*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:
  
== August 13, 2020 ==
+
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
  
=== Species in Postgres and ACEDB/Datomic ===
+
making sure to enter the variation with name-space-WBVarID like:
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
 
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
 
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
 
* We currently have multiple Postgres tables for storing species lists:
 
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
 
** obo_name_ncbitaxonid
 
** obo_name_taxon (original, smaller list)
 
** h_pap_species_index (history for pap_species_index)
 
* How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
 
* WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
 
* Kimberly used to upload a species.ace file; now Hinxton handles it; should ask them
 
  
=== WS279 Citace upload ===
+
gk315316 WBVar01148785
* When is it happening? Not sure; not on release schedule right now
+
 
 +
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

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