Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(319 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
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
== June 10, 2021 ==
  
 +
=== 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
  
== September 3, 2020 ==
+
===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 ?)
  
=== WS279 Citace upload ===
+
*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:
* September 25
 
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
 
  
=== New AFP datatype for curation status form (CSF)? ===
+
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
* afp_othergenefunc (to capture gene function other than enzymatic activity)
 
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
 
  
=== GO annotation for description ===
+
making sure to enter the variation with name-space-WBVarID like:
* Kimberly will look into 'male tail tip developement' terms for description
 
  
=== Migrate wobr1 server to AWS ===
+
gk315316 WBVar01148785
* SOLR, WOBr, SObA, Enrichment analysis
 
* Working with Sibyl on the process
 
* Will try migrating wobr1 first, as a test case
 
* May eventually move, for example, Tazendra
 
** Will there be drawbacks to doing this?
 
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
 
* Don't yet know the details of the costs, but we can try and keep track
 
* We should move into WB or Alliance AWS instances (or Stanford)
 
  
=== WormBase talk at Boston Area Worm Meeting ===
+
and then, after refresh, it should be available to the OA. Hinxton never has to get involved in this scenario.
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 
* Meeting will be virtual on Zoom
 
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 
* Send topic requests to Chris for the talk
 
* Current topics:
 
** Micropublications
 
** Author First Pass
 
** Automated Gene Descriptions
 
** Community Curation
 
** WB Query Tools
 
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
 
  
 +
=== Confirm WS282 Upload Dates ===
 +
*July 6th?
 +
*Data freeze/upload date on the release schedule is July 12th
  
== September 10, 2020 ==
+
=== 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
  
=== GO GAF Files ===
+
* Bring in data both as pictures and interactive bar plots
* WS278 GO GAF is using the new 2.2 file format
+
* Ping Hinxon on GitHub to move this forward
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
 
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
 
* Implications for gene descriptions, but what about other tools, applications at WB?
 
* Some errors in the current WS278 GAF, but will get fixed soon
 
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
 
 
 
===Disease files on FTP===
 
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
 
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
 
 
 
=== WormBase talk at Worcester Area Worm Meeting ===
 
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
 
* 30 minute slot; complementary to BAWM talk?
 
* WormBase members can attend
 
 
 
=== WormBase talk at Boston Area Worm Meeting ===
 
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 
* WormBase members can attend; Zoom link will be sent next Monday
 
 
 
=== Worm Anatomy Ontology Fixes ===
 
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
 
* Assessing the best way to address them
 
* Would be good to be able to automate some edits; options:
 
** Use OWL API (need someone proficient in coding with OWL API)
 
** Convert to OBO, programmatically edit, convert back to OWL?
 
** Use Cellfie plugin for Protege?
 
** Should discuss with Nico once we have a sense as to what changes need to be made
 
 
 
=== Dead Variations in Postgres ===
 
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
 
* Noticed that many transgene names were being included, which can result in false positives for the categories
 
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
 
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
 
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
 
* We could use pattern matching to filter out transgene names
 
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
 
 
 
=== WS279 Citace Upload ===
 
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
 
 
 
 
 
== September 17, 2020 ==
 
 
 
=== Species errors in CITace ===
 
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
 
 
 
=== Webinars ===
 
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
 
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
 
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP
 
* Chris and Wen can discuss how to setup
 
* Should we have people register? Maybe
 
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
 
 
 
=== Transcription factors and regulatory networks ===
 
* Had another question about TFs, asking for common TFs for a list of genes
 
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
 
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
 
 
 
=== Alzheimer's disease portal ===
 
* Funding has been awarded for Alzheimer's research
 
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
 
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
 
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
 
* Ruth Lovering is doing some work in this regard
 
 
 
=== GO meeting ===
 
* All are welcome to attend
 
* Will discuss GAF format changes, etc.
 

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