WBConfCall 2020.03.05-Agenda and Minutes

Agenda & Minutes

Project meeting

• 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)

WS277 data freeze

• 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)

Help Desk

• 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)?
      • GO annotations added to Y53C10A.5 using WBPaper00059383 as evidence (2020-03-09 kmva)
• CGC bad WB link URL; can this be closed?
  • Kimberly will follow up and then close
    • Link fixed and issue now closed (2020-03-09 kmva)
• 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

Rearrangement IDs

• 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

Nameserver-to-Caltech info transmission

• 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; may look in WormBase, if not there, go to Name service; try to generate an ID, if exists will get a notice, if not, an ID will be generated an used in CGI to immediately import into Postgres/OA, need to refresh OA to see the variation
  • Genetics and G3 papers and microPublications need linking for objects; if not already in DB, create in Name service and create link

Disease info changes in 6 classes

• 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

Single cell expression tool

• 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
• Should send around to users who have asked about single cell data (e.g. Peter Roy)