Revision as of 17:17, 5 March 2020

Agenda & Minutes

Hinxton attendance in doubt
- EMBL Coronavirus guidelines: do not plan any unavoidable travel
Could important subsets of the agenda be done virually
Paul S: Travel looks like it's going to slow down due to restrictions
- We should consider how to do the meeting remotely/virtually
- Maybe we can do a conference call late March or early April
- Could try one topic per day 2-3 hours each time (early for California, late for UK)
- Will take some discipline and focus, but we can get it done
- Taxis can be arranged for travel after public transport hours (still a lot cheaper than trans-Atlantic flights)

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
Will WS276 go to FTP site this weekend?
- There have been some delays, so probably won't be up until next week sometime (definitely up by March 13)

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?
- Kimberly will follow up and then close
Maureen Barr's question about protein coding genes with known function; can this be closed?
- Kimberly will follow up and then close
Setting up local instance of JBrowse; can this be closed?
- Scott hasn't heard back, will close for now

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
We want to make sure that users can still find the Rearrangement objects as they have in the past; e.g. web pages, tracks in the genome browser for balancers, etc.
Rearrangements have been historically difficult to map; will mapping become a problem
Karen, Paul, et al. will setup a call

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.
Easiest current solution is to make the new Strain addition CGI, but still not ideal
Could possibly implement the OA to make requests to the Name service but would require login using wormbase.org Google accounts, but would likely take a considerable amount of code writing
Karen use case:
- Phenotype curation; try to enter into the OA, doesn't come up; look in WormBase, if not there, go to Name service; query to see if it already exists, if not create to generate an ID, use CGI to immediately import into Postgres/OA
- Genetics and G3 papers and Micropublications need linking for objects; if not already in DB, create in Name service and create link

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)
https://wiki.wormbase.org/index.php/Model_changes_to_capture_and_consolidate_human_disease_data

Eduardo is looking for feedback on his tool to query C. elegans single cell expression
Tool is here: http://de.wormcells.com/
Can produce volcano plots
- x axis log2 expression
- y axis base factor (generalization of a p-value)
  - Anything above 2 or 3 is a robust hit

@@ Line 67: / Line 67: @@
 * Eduardo is looking for feedback on his tool to query C. elegans single cell expression
 * Tool is here: http://de.wormcells.com/
+* Can produce volcano plots
+** x axis log2 expression
+** y axis base factor (generalization of a p-value)
+*** Anything above 2 or 3 is a robust hit