WBConfCall 2023.03.02-Agenda and Minutes

Help Desk

• #8959 Is it possible to get WS276 JBrowse again?
  • Scott set it up on a dev site.
• #8965 I have tried downloading gene data to CVS or any other format. It only shows html format. It seems to be the links for all buttons are broken.
  • This is probably related to the Caltech power outage today.
• #8966 C. inopinata ortholog info?
  • Scott responded.

S. ratti community curation

• What is the current WormBase-preferred method of receiving community-driven manual curation data for S. ratti and what types of changes are sufficient?
  • Researchers can keep a slim version of GFF and a CSV about gene info including gene history and information needed to update gene pages. These can be stored on github
  • Wen and Hinxton will communicate with them about setting a standard of community curation.
• Gene pages at the Alliance
  • Would minimally require a Basic Gene Information (BGI) JSON submission to the Alliance File Management System (FMS)
  • BGI entries minimally require primary key (curie), taxon, symbol, and SO term
  • agr_schema ingest JSON specifications: https://github.com/alliance-genome/agr_schemas/tree/master/ingest
    • gene.json specification: https://github.com/alliance-genome/agr_schemas/blob/master/ingest/gene/gene.json
    • basicGeneticEntity specification: https://github.com/alliance-genome/agr_schemas/blob/master/ingest/basicGeneticEntity.json

C. briggsae

• piRNAs from Wen Tang (Ohio State University College of Medicine) https://github.com/WormBase/website/issues/8962
  • Researchers can generate GFF and Scott can load it into WormBase asap
  • No need to create gene pages for them

New elegans assemblies

• VC2010 (CGC1) from Erich Schwarz (Cornell)
  • Is it time for us to switch over?
• 20 new assemblies from Cristian Riccio (Sanger) https://github.com/WormBase/website/issues/8958
  • Need to discuss this at a future Advisory Board meeting

IWM 2023

• Parasite workshop invites WormBase to participate in their discussion on how to establish gold standards on parasite community curation.
  • Hinxton people will be there
• WormBase workshop approved. We need to decide on speakers.

WormBase ParaSite

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• Posted on WB blog

REST API Broken

• It was caused by tazendra down caused by the Caltech power outage at the Chen building
• Juancarlos and Valerio are migrating tazendra to a dockerized server