WBConfCall 2024.02.01-Agenda and Minutes
Agenda/Minutes
Helpdesk Issues
- [Addressed by Stavros and Cecilia] Colin Dolphin can't login to WormBase https://github.com/WormBase/website/issues/9417
- Everything seems ok
- [Possibly not addressed, Stavros self-assigned] snpc-1.4 misannotated https://github.com/WormBase/website/issues/9418
- Stavros is on it
- [Addresed by Wen] Transposon name map question (David Meyer)
- [Addressed by Ranjana] Gene descriptions - functional description of human orthologs https://github.com/WormBase/website/issues/9421
- [addressed by Wen] export the data points for the "FPKM expression data from selected modENCODE libraries" https://github.com/WormBase/website/issues/9420
- [Addressed by Cecilia] Michael Ristow wants to update contact info https://github.com/WormBase/website/issues/9416
- [Addressed by Wen and Raymond] GSEA for enrichment analysis https://github.com/WormBase/website/issues/9415
Agenda Items
- Alliance code security warnings (notification by Michael Paulini through wormbase-help) - OICR?
- dependabot emails on npm libraries. Chris will take a look. - remove people from repos after they leave the Alliance/WB
- Invalid LAB and allele designations sneaking into WormBase - advice needed please. #9409 [SKD]
[Tim] Strains with invalid strain names and allele names should not be curated.
[Karen] The strains are real so they should be captured. However the authors need to rename them to adhere to our nomenclature rules, regardless, so they need to be contacted for sure. I would vote to NOT curate the strains unless the authors change the names, but for the one that has been curated, remove the name from the public_name field, leaving that blank, since the strain has a WBStrainID it is trackable. Add the incorrect name into a remark field.
[Stavros] will check how many there are for WS293. [Ranjana] asks how many there are from caltech before deciding. [Paul] We should contact journals to enforce this (through automation)
- Updating the C. elegans ribosomal subunit gene names and protein names. [Tim]
Tim found examples where orthology was wrong in ribosomal units and subunits. He got in contact with people who studies ribosomal genes in worm and they want to be able to search WB with the ribosomal gene name and get the right gene. They use structural proitein names that are not the standard protein names. Tim asks to add a synonym for those protein names. [Chris] It could be included in the "other name" field. [Tim] That would work if it is the easiest solution. [Todd] That would make search work out of the box. [Paul] is there a reference for the naming scheme? [Tim] Yes. [Paul] We could ask for a micropublication with just the table of these protein sequence names. [Tim] Certainly.
- BLAST service Alliance/WB
It is currently in both places. There's a new link from WB to BLAST. We should also add more visibility from the Alliance
