Difference between revisions of "WBConfCall 2023.09.21–Agenda and Minutes"
From WormBaseWiki
Jump to navigationJump to search| Line 52: | Line 52: | ||
* 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. | * 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. | * 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. | + | * 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. Could figure things out from publication trends. |
| + | * Raymond - Also biocuration automation. | ||
| + | * Sarah - With Magda would look at datatypes and figure out what would or wouldn't have a home. Apollo coming in as we move away from ace needs discussion and defining. | ||
| + | * Paul - Discussion about sequence and Apollo. | ||
| + | * Sarah - Apollo has a lot of backend and not much front end, so not very usable. Nothing before 6 (?) months. | ||
| + | * Stavros - Some developer changes at Apollo. | ||
| + | * Paul - If not for 1.5 years, is it close enough to freeze what we have until then. | ||
| + | ** Need Apollo to handle other species. | ||
| + | ** What do we want in 2 years. | ||
| + | ** Plan that out, then figure out timeline and transition. | ||
| + | * Stavros - Feb 2024 was timeline, but probably won't happen. | ||
| + | * Paul - A 6 month gap is okay. Good Stavros is helping Apollo. If it's good in 1.5 years, how will that look. | ||
| + | * Sarah - Still need to figure out how Apollo will communicated with Alliance. | ||
Revision as of 16:01, 21 September 2023
Contents
Agenda
Help Desk
- https://github.com/WormBase/website/issues/9322
- Paulo will take a look
Sequence feature curation
- 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
ftp site synchronization
- 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
Caltech-Nameserver options
- How should Variation and Strains be created by Caltech curations, what options are possible.
Minutes
Sequence Feature Curation
- 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.
ftp site synchronization
- 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.
Caltech-Nameserver options
- Hoped to talk with Caltech curators and Manuel about Caltech-Nameserver, but people are at Machine Learning in Biocuration workshop.
What can we do about transferring things to Alliance taking so long.
- 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. Could figure things out from publication trends.
- Raymond - Also biocuration automation.
- Sarah - With Magda would look at datatypes and figure out what would or wouldn't have a home. Apollo coming in as we move away from ace needs discussion and defining.
- Paul - Discussion about sequence and Apollo.
- Sarah - Apollo has a lot of backend and not much front end, so not very usable. Nothing before 6 (?) months.
- Stavros - Some developer changes at Apollo.
- Paul - If not for 1.5 years, is it close enough to freeze what we have until then.
- Need Apollo to handle other species.
- What do we want in 2 years.
- Plan that out, then figure out timeline and transition.
- Stavros - Feb 2024 was timeline, but probably won't happen.
- Paul - A 6 month gap is okay. Good Stavros is helping Apollo. If it's good in 1.5 years, how will that look.
- Sarah - Still need to figure out how Apollo will communicated with Alliance.
