Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2021 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
+
= 2022 Meetings =
 
 
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
 
  
[[WormBase-Caltech_Weekly_Calls_November_2021|November]]
+
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
[[WormBase-Caltech_Weekly_Calls_December_2021|December]]
 
 
 
= 2022 Meetings =
 
  
 
= January 13th, 2022 =
 
= January 13th, 2022 =
 
== tm variation - gene associations ==
 
== tm variation - gene associations ==
 
*Update on progress and some questions for the Caltech curators
 
*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.
 +
**https://github.com/WormBase/website/issues/8262
 +
**https://wiki.wormbase.org/index.php/WBGene_information_and_status_pipeline
 +
**https://wiki.wormbase.org/index.php/Source_and_maintenance_of_non-WBGene_info
 +
**https://wiki.wormbase.org/index.php/Updating_Postgres_with_New_WS_Information
 +
*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 [https://academic.oup.com/g3journal/article/11/3/jkab022/6121926 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?
  
== December 16 2021 ==
+
= January 20th, 2022 =
 
 
=== tm variation - gene associations ===
 
*Not all tm variation - gene associations are in the nightly geneace dump
 
*We need to retrieve the remainder from WS
 
*WS updates to postgres have apparently not been working for some time; script for downloading WS is not working
 
*We need a better way to get the WS updates
 
*Query WS on spica? automatically generate files from queries of WS on spica?
 
*Future proof: (when) should we start thinking about querying the Alliance, instead?
 
  
=== protein-containing complexes in WB ===
+
== Proposal for updating gene and variation information from WS releases ==
*The Complex Portal (EBI) group makes GO annotations to C. elegans protein-containing complexes
+
=== Genes ===
**448 annotations to 132 unique protein-containing complexes
+
*Have two tables:
**We currently can't do anything with these annotations, although we will be able to bring in derived annotations to the individual members (once evidence code issues get sorted out)
+
**One continues as is - contains only ids for the [https://wormbase.org/species/all core nematode species] (all have WBGene ids)
*What do we think about instantiating protein-containing complexes in WB?
+
**Second, new table - contains non-WGene ids for [https://wormbase.org/species/al comparator nematode genomes]
*How would this fit into the Alliance roadmap?
+
***Include other elegans and remanei strains?
 +
**Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast
 +
=== Variations ===
 +
*Include all variations that have a value for:
 +
**Method - current filters applied (filter SNP, Million_mutation, WGS's)
 +
**Species - all
 +
**Status - include all three status values (Live, Dead, Suppressed)
 +
*Whether a variation has a gene association doesn't matter (not a filter criteria for postgres)
 +
*From Paul D. - a number of variations in geneace were not making their way as individual objects to WS during the build and so were only created in WS via xref (hence the lack of other information). He's updated geneace with Species and other information wherever possible for the next build.
 +
*Variation merges are infrequent; previous ones may have been due to nameserver issues
 +
*New Methods arise infrequently, but we could check our parsing script against the list of Methods in each release to make sure we're up-to-date.  Would need an inclusion and exclusion list.

Revision as of 15:24, 20 January 2022

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

2022 Meetings

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?

January 20th, 2022

Proposal for updating gene and variation information from WS releases

Genes

  • Have two tables:
    • One continues as is - contains only ids for the core nematode species (all have WBGene ids)
    • Second, new table - contains non-WGene ids for comparator nematode genomes
      • Include other elegans and remanei strains?
    • Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast

Variations

  • Include all variations that have a value for:
    • Method - current filters applied (filter SNP, Million_mutation, WGS's)
    • Species - all
    • Status - include all three status values (Live, Dead, Suppressed)
  • Whether a variation has a gene association doesn't matter (not a filter criteria for postgres)
  • From Paul D. - a number of variations in geneace were not making their way as individual objects to WS during the build and so were only created in WS via xref (hence the lack of other information). He's updated geneace with Species and other information wherever possible for the next build.
  • Variation merges are infrequent; previous ones may have been due to nameserver issues
  • New Methods arise infrequently, but we could check our parsing script against the list of Methods in each release to make sure we're up-to-date. Would need an inclusion and exclusion list.