Difference between revisions of "WBConfCall 2020.08.20-Agenda and Minutes"

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* Help with annotation file for ws235 version
 
* Help with annotation file for ws235 version
 
** Email on Monday Aug 17
 
** Email on Monday Aug 17
** Need something parsed from GFF.  Raymond will ask who sent them the original file.  Exon Rank is an ensembl thing, might be from ensembl-biomart, not WormBase.
+
** Need something parsed from GFF.   
How much formatting do we owe users, could give a GFF3 and let them figure it out. On ws220 they may have used WormMart, which we don't have anymore. "It loo
+
** Raymond will ask who sent them the original file.   
ks like you used a service we don't provide anymore, we have the data in a different format, is that okay"
+
** Exon Rank is an ensembl thing, might be from ensembl-biomart, not WormBase.
 +
** How much formatting do we owe users, could give a GFF3 and let them figure it out.
 +
** On ws220 they may have used WormMart, which we don't have anymore.
 +
** "It looks like you used a service we don't provide anymore, we have the data in a different format, is that okay"

Revision as of 15:47, 20 August 2020

Agenda

WS279 Data Freeze

  • When?

Help Desk

Handling species lists

  • Handling species in WormBase and Alliance
    • Want to dump "affected_by_pathogen" field for phenotypes listing pathogenic species
    • Want/need to synchronize Postgres with Hinxton and ACEDB
    • Would like a primary species list
    • Should clean up existing species data, then possibly move to a centralized species tool at the Alliance
    • Source data: NCBITaxonomy
      • There is some churn on taxonomy ids, e.g. one taxonomy id is merged into another (although it appears to be relatively infrequent compared to other CVs or ontologies)
      • We will need a plan for tracking changes and updating our curation data as needed

Minutes

WS279 Data Freeze

  • Michael WS 279 dependent on when the 278 build finishes. WS 278 hopefully done end of next week or soon after.

Help Desk

  • uncharacterized eukaryotic protein-coding gene with an intron
  • Help with annotation file for ws235 version
    • Email on Monday Aug 17
    • Need something parsed from GFF.
    • Raymond will ask who sent them the original file.
    • Exon Rank is an ensembl thing, might be from ensembl-biomart, not WormBase.
    • How much formatting do we owe users, could give a GFF3 and let them figure it out.
    • On ws220 they may have used WormMart, which we don't have anymore.
    • "It looks like you used a service we don't provide anymore, we have the data in a different format, is that okay"