Difference between revisions of "WormBase-Caltech Weekly Calls"

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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 dump.  Some variation-gene associations are made as part of the VEP pipeline during the build.
 
*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://github.com/WormBase/website/issues/8262
*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.
+
*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:
 
*A few questions that we want to confirm before going forward:
 
**For the variations, do we only want in the obo table only those variations that have a gene association (either in geneace or WS) or do we want all variations?
 
**For the variations, do we only want in the obo table only those variations that have a gene association (either in geneace or WS) or do we want all variations?

Revision as of 16:25, 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.
  • https://github.com/WormBase/website/issues/8262
  • 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:
    • For the variations, do we only want in the obo table only those variations that have a gene association (either in geneace or WS) or do we want all variations?
      • The effect on the autocomplete, if we include all, probably won't be a problem.
      • Currently, some variations with a given Method, e.g. Million_mutation, are NOT included. Are there any other filters we want, e.g. species?
    • 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, lesser 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?
      • The effect on the autocomplete, if we include all, probably won't be a problem.
      • 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?