WBConfCall 2023.09.21–Agenda and Minutes

Agenda

Gary Williams was curating sequence features for expression annotations, for example enhancer regions sufficient to drive expression in a certain tissue.
We are not actively curating this at the moment but there are a couple of annotations that need Sequence Feature objects -found while cleaning up data for Alliance.
In the short term there would be need to curate only Sequence Feature objects for these 2 existing papers, but to do so would need access to the F map?
Example of a sequence feature connected to expression: https://wormbase.org/species/all/expr_pattern/Expr11278#02--10
https://github.com/WormBase/website/issues/9328

GO is waiting for the WB GAF to complete their September release
Are there still problems with synchronizing the Hinxton and WB ftp site?
- If so, can we temporarily point GO to the Hinxton ftp site or will they have the same problem?
https://github.com/WormBase/website/issues/9319

How should Variation and Strains be created by Caltech curations, what options are possible.

Daniela - Cannot do full seq feat curation, but could curate a few here and there, but how to access tools for it.
Stavros - Enhancement curated in geneaces. Can look at documentation. Gary left a couple of guides. It will take some time, try before next build starts.
Daniela - Not urgent, for transfer of expression data at Alliance to persistent store. Only objects associated to genes for now. Have some months.* Stavros - github ticket helps keep it in mind. Maybe for 292.

Stavros - ftp error at EBI probably from ddos attack, admins have it working again.
Paulo - Tried to sync symlinks, but most of OICR is owned by Todd (not at meeting), so not sure it's synced properly, waiting to hear from him. Could manually sync specific files Kimberly needs.
Stavros - http and https should work.
Paulo - Sync is all through perl, but not working well right now. Can see Aug 31st files from last sync. Will take a look.

Hoped to talk with Caltech curators and Manuel about Caltech-Nameserver, but people are at Machine Learning in Biocuration workshop.

Paul S - Alliance won't have a home for most of the data for a while. Should we keep curation going or save energy from the build.
Todd - Can't have a partial build.
Paul - How much data do we need before we can stop doing the build.
- Not much RNAi data, now more crispr.
- In the context of Genetics article and for planning, go through all datatypes, figure out what's missing in Alliance.
- Some stuff won't get organized, like Cengen, it's about UI switch and will handle separately. Will take work, but not need A-team.
- Go through everything class by class and see what's worth doing. Find some temporary solutions if necessary.
Todd - How much is getting curated per dataclass, if not active... (maybe don't worry about it ?)
- Users can have separate Alliance and WB browser tabs open.
- Gene name changes are important.
- Make changes available from Caltech.
Paul - Point to users about what's missing at Alliance.
Todd - Invert user flow, instead of starting at WB, start at Alliance.
Paul - Curation, figure out what's active. We'd like to curate this, but instead do GO-Cam or something else. Until the Alliance persistent store

can handle curation. We have more curation that needs doing than we can do.

Sarah - What's the granularity of what users need more, prioritize based on user use.
Todd - Could do that, but not that easy to figure out, e.g. the gene page has lots of data and don't know what users are looking at.