WBConfCall 2024.01.18-Agenda and Minutes

Agenda/Minutes

Helpdesk Issues

• Jonathan Ewbank wants to change his primary contact on the website.
  • Paulo could edit the DB directly. Objections? Paulo will check in with Todd.
  • https://github.com/WormBase/website/issues/9407
• Strain CF439 issue
  • Aric will sequence the oldest stock of CF439 that they have
  • Based on the results we will update our records
  • https://github.com/WormBase/website/issues/9410
• Extracting small molecule interaction data
  • Any way to systematically extract small molecule interaction data? Specifically, I am looking for data about small molecules that can suppress lethal phenotypes.
  • https://github.com/WormBase/website/issues/9408

Agenda Items

• Stage Literature AGRKB related bug. Same WBPaperID two different papers. See details on Slack #general Monday, 15 January [Stavros]
  • Is this related to https://github.com/WormBase/website/issues/9398 (clean-up of WBPaper IDs)?
  • Daniela: It shouldn't be related as #9398 was about Micropubs and Genetics articles
• Kudos to the Alliance literature DB from Stavros!
• WormBase Genetics paper reviewer's feedback

• Invalid LAB and allele designations sneaking into WormBase https://github.com/WormBase/website/issues/9409 [Stavros]
  • Find better ways to prevent incorrect strain designations
  • Use Cecilia's lab data to have the most up-to-date list of approved strain names
  • To try to plug the problem from the source, we should ask CGC to include a nomenclature note with the strains they send out. Asking people to follow our guidelines.
  • The temp_objects.cgi is going to go away and replaced by what Manuel creates, so it would be good if whoever wants to spec it, would also tell them to make the object restriction be however you want it to be, so he knows how to make it
  • For now curators should go to the laboratory field in any OA that has it (for example Antibody) or to the laboratory form (https://caltech-curation.textpressolab.com/priv/cgi-bin/cecilia/lab_editor.cgi) or Tim's email.

• [To be discussed once Tim is present, probably on Feb 1st] New additions to Gene or Protein class (Structural biology ribosomal protein names) https://github.com/WormBase/website/issues/9400 [Stavros, Tim]
• what is happening with the phenotype submission forms? The data is still going to Caltech and not to the cloud CGI. Paulo and Todd need to look into it. Paulo says that the new code should be on staging, it should be released tomorrow. Paulo will also check with Juancarlos. Is there a links list? On the WB homepage -> Submit data
• Stavros will be out next week, working on CGC updates, alleles.. The build will be pushed probably one week and the WS292 can be a bit late. All good, no problem.