Difference between revisions of "WBConfCall 2023.09.21–Agenda and Minutes"

Revision as of 15:46, 21 September 2023

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.

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.

@@ Line 22: / Line 22: @@
 ==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.