Revision as of 15:26, 5 March 2020

Agenda

When will the schema be released?
- Scheduled for 13th March
- Upload 3rd April
- Can be flexible and push back by a week if required.
Several Caltech curators may take March 30 - April 3 off due to school break

The following 3 items are linked and the Gene has been named and a new lab created:
- Has anyone replied to Padhu Padmanabhan (email Feb 4)? - Yes Paul D. replied on the 4th directing them to the genenames list
- Asked about indicating Y53C10A.5 as having plasmanylethanolamine delta-1-desaturase (EC 1.14.99.19) activity - Can be closed
- Has anyone replied to Montserrat Elías regarding naming of same gene, Y53C10A.5? - This name has been agreed by Tim S. and the issue can be closed.
- Unsure on this:
  - Could this be added as a GO MF (GO:0050207)?
CGC bad WB link URL; can this be closed?
Maureen Barr's question about protein coding genes with known function; can this be closed?
Setting up local instance of JBrowse; can this be closed?

From thread on Slack, "general" channel
Karen asked about getting WB IDs for rearrangements (they currently do not get serial IDs)
Todd suggested rolling them into the WBVariation class
Rearrangement class model doc https://docs.google.com/document/d/1Zntv3UA30dYxyf0MLKgZnThlFMPdTJ_wOokD06vdxss/edit?usp=sharing

Caltech curators would like quick turn around when requesting names/IDs
Currently relies on a nightly cronjob to dump GeneACE to Caltech Postgres database
Caltech can create a local CGI to immediately update Postgres/OA with new terms before nightly dump occurs
Is there an effective mechanism to make updates to Caltech Postgres/OA as immediately as possible?

- The Nameservice is available for curators to request IDs so they can immediately continue with curation.
- Extend the TempVariationObo system to all classes
- Potential for a queue system so that they get automatically added (Prototype system was added for different purpose but pulled a long time ago).
- The rest API could be used to request IDs direct from the OA meaning that they would be available immediately without relying on additional services.

I propose making these changes for WS278, gives us more time to revisit/change dumpers, and test the data here at Caltech (Ranjana)
If we want to go ahead with the new ?Genotype class, that's separate and I'm fine with that (Ranjana)

Eduardo is looking for feedback on his tool to query C. elegans single cell expression
Tool is here: http://de.wormcells.com/

@@ Line 13: / Line 13: @@
 ** Asked about indicating Y53C10A.5 as having plasmanylethanolamine delta-1-desaturase (EC 1.14.99.19) activity - Can be closed
 ** Has anyone replied to Montserrat Elías regarding naming of same gene, Y53C10A.5? - This name has been agreed by Tim S. and the issue can be closed.
+** Unsure on this:
-* Unsure on this:
+*** Could this be added as a GO MF (GO:0050207)?
-** Could this be added as a GO MF (GO:0050207)?
+* [https://github.com/WormBase/website/issues/7581 CGC bad WB link URL]; can this be closed?
+* [https://github.com/WormBase/website/issues/7579 Maureen Barr's question about protein coding genes with known function]; can this be closed?
+* [https://github.com/WormBase/website/issues/7578 Setting up local instance of JBrowse]; can this be closed?
 == Rearrangement IDs ==