Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
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= 2022 Meetings =
  
= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
  
==January 11th, 2019==
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= January 13th, 2022 =
 
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== tm variation - gene associations ==
===WB workshop at IWM 2019===
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*Update on progress and some questions for the Caltech curators
Here's a draft, need to finalize as Jan 15th is the deadline
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*Background: not all variations were being associated with genes in the OA table because some of those associations are in WS but not in geneace, so weren't coming through in the nightly geneace dumpSome variation-gene associations are made as part of the VEP pipeline during the build.
<pre style="white-space: pre-wrap;
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**https://github.com/WormBase/website/issues/8262
white-space: -moz-pre-wrap;
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**https://wiki.wormbase.org/index.php/WBGene_information_and_status_pipeline
white-space: -pre-wrap;
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**https://wiki.wormbase.org/index.php/Source_and_maintenance_of_non-WBGene_info
white-space: -o-pre-wrap;
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**https://wiki.wormbase.org/index.php/Updating_Postgres_with_New_WS_Information
word-wrap: break-word">
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*Wen now downloads several full ACeDB classes from the latest WS release in the form of .ace files so we can also have whatever information is in WSRaymond wrote a script to sync those files to tazendra for further processing/use.
Possible Title 1: Data in WormBase and how to query it
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*A few questions that we want to confirm before going forward:
Possible Title 2: WormBase 2019 - Data, Tools and Community Curation
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**In the WS variations file, there are 2,130,801 total variations (1,911,339 total Live) while in postgres there are currently 106,080.
This workshop will be an interactive session with users in order to discuss the types of data in WormBase and how to query them using the right tools.  We will discuss recent changes to WormBase community annotation forms and how to use them to contribute data to WormBase.  We will also present updates to ParaSite, a portal to parasitic worm genomic data, and how to find cross-species data at the Alliance of Genome Research.
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***Only include Status = Live variations?
 
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***Include regardless of whether there is an associated gene (this seems to be the current practice?).
1:00 pm  
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***Currently, some variations with a given Method, e.g. Million_mutation, are NOT included.  We would continue this filtering.
Keep your widgets open: a wealth of gene-related data on the gene page
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****SNP
(This will be a quick walk-through of the gene page for orienting Users before we jump into the tools; can point to data related to Gene function, expression and disease models) - Ranjana Kishore
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****WGS_Hawaiian_Waterston
     
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****WGS_Pasadena_Quinlan
1:10 pm 
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****WGS_Hobert
Use the right tool for the right data:
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****Million_mutation
Get simple lists using SimpleMine - Wen Chen
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****WGS_Yanai
Tissue enrichment analysis tools - Kimberly Van Auken
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****WGS_De_Bono
Tools for RNA seq data - Wen Chen
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****WGS_Andersen
Get batch gene data using the WormBase Ontology Browser - Raymond Lee
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****WGS_Flibotte
Get the big picture: visualize annotations using the SOBA tool -Raymond Lee
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****WGS_Rose
     
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***Do we want other filters?
1.50 pm  WormBase ParaSite: Exploring lots of genomes - Kevin Howe
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**For genes, the ace file contains ALL the gene objects in WB regardless of species.
 
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***We've recently had an author request, via the Acknowledge pipeline, to associate genes of other, less well studied Caenorhabditis species, e.g. C. inopinata, to [https://academic.oup.com/g3journal/article/11/3/jkab022/6121926 their paper].
2.00 pm  Find cross-species data at the Alliance of Genome Research - Chris Grove
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***Do we want all Caenorhabditis (and other nematode) species genes in our various gene tables, e.g. obo, paper? Any other species?
 
+
***The effect on the autocomplete, if we include all, probably won't be a problem 1,018,332 vs 306116)
2.10 pm Be a Community Curator: submit your data to WormBase - Daniela Raciti
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***Some of the gene ids from other species don't have 'WBGene' prefixes, e.g. Sp34_10109610.  Should we keep this in a separate table from genes with 'WBGene' prefixes?
 
 
2.10-2.30pm. Open forum for questions
 
</pre>
 
 
 
=== Finalize Protege tutorial time ===
 
* Best final options:
 
** Wed, Jan 16th, 1pm Pacific/4pm Eastern
 
** Thurs, Jan 17th, 11am Pacific/2pm Eastern
 
** Thurs, Jan 17th, 1pm Pacific/4pm Eastern
 
* Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern
 
 
 
== January 3, 2019 ==
 
 
 
=== WS270 Citace upload ===
 
* Next Tuesday, Jan 8th, 10am Pacific
 
 
 
=== Gene descriptions ===
 
* Valerio generated new files to ignore/filter-out problematic genes
 
* Still need to validate new pipeline
 
* Barring any major issues, will submit new files for WS270 (can load old files if needed)
 
* Maybe should define a test set (random sample) to test each release? Already have a test set
 
 
 
=== Protege Tutorial ===
 
* Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
 
* Please fill out poll if you are interested in attending; have responses from Kimberly and Gary S.
 

Latest revision as of 18:56, 13 January 2022

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January

January 13th, 2022

tm variation - gene associations

  • Update on progress and some questions for the Caltech curators
  • Background: not all variations were being associated with genes in the OA table because some of those associations are in WS but not in geneace, so weren't coming through in the nightly geneace dump. Some variation-gene associations are made as part of the VEP pipeline during the build.
  • Wen now downloads several full ACeDB classes from the latest WS release in the form of .ace files so we can also have whatever information is in WS. Raymond wrote a script to sync those files to tazendra for further processing/use.
  • A few questions that we want to confirm before going forward:
    • In the WS variations file, there are 2,130,801 total variations (1,911,339 total Live) while in postgres there are currently 106,080.
      • Only include Status = Live variations?
      • Include regardless of whether there is an associated gene (this seems to be the current practice?).
      • Currently, some variations with a given Method, e.g. Million_mutation, are NOT included. We would continue this filtering.
        • SNP
        • WGS_Hawaiian_Waterston
        • WGS_Pasadena_Quinlan
        • WGS_Hobert
        • Million_mutation
        • WGS_Yanai
        • WGS_De_Bono
        • WGS_Andersen
        • WGS_Flibotte
        • WGS_Rose
      • Do we want other filters?
    • For genes, the ace file contains ALL the gene objects in WB regardless of species.
      • We've recently had an author request, via the Acknowledge pipeline, to associate genes of other, less well studied Caenorhabditis species, e.g. C. inopinata, to their paper.
      • Do we want all Caenorhabditis (and other nematode) species genes in our various gene tables, e.g. obo, paper? Any other species?
      • The effect on the autocomplete, if we include all, probably won't be a problem 1,018,332 vs 306116)
      • Some of the gene ids from other species don't have 'WBGene' prefixes, e.g. Sp34_10109610. Should we keep this in a separate table from genes with 'WBGene' prefixes?