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.

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

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

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

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.

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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