WBConfCall 2020.08.20-Agenda and Minutes

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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


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 loo

ks like you used a service we don't provide anymore, we have the data in a different format, is that okay"