WormBase-Caltech Weekly Calls

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June 3, 2021

Reserving meeting rooms

  • Raymond encountering challenges with setting up regular meeting room reservations in Chen building
  • We've been asked to make reservations one week in advance
  • Need to use a room if we reserve it

Summer student(s)

  • Anatomy function project with Raymond
  • Many types of anatomy function data submitted via AFP

June 10, 2021

Variation-Gene Associations

Variation in name service but not in OA

  • Ranjana: I could not find gk315316 in the OA though it exists in the name server. I agree that we probably don’t want to let all the million mutations into the OA since that would slow the drop-downs, but when we need one for curation, what needs to be done?
  • Juancarlos: That might be right. It seems to try to create the variation in the name service, and if it gets a 409 Conflict error, it adds it to the temp variation file, and the obo_ tables in postgres. Since it fails to create in the name service, that's probably okay with Hinxton, and since it gets added to postgres, you should be able to use it in the OA, and since it gets added to the temp variation file, on future updates of the ontology it gets added again. Probably best if someone confirms that's the process (and maybe points us to a wiki ?)

Confirm WS282 Upload Dates

  • July 6th?
  • Data freeze/upload date on the release schedule is July 12th

CenGen bar plots

  • Initially discussed to have the bar plot images going in as image data
  • CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
  • They can provide the underlying data and have the WB team generate interactive plots for each gene
  • Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
  • The first approach may be more work but better in the long run as we store the data
  • Will ping Hinxton and see how they can integrate the data