WBConfCall 2022.03.17-Agenda and Minutes

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Agenda

Help Desk

  • Julie Ahringer asking for a genome-wide mapping of all Ahringer RNAi clones (sjj_* and sjj2_* ?PCR_Product objects) to identify, according to our primary and secondary RNAi mapping criteria, which genes are predicted to be knocked down by each clone

- Hinxton are in touch with her to scope out the size and timing of the work.[MZ]

Minutes

Julia Ahringer

  • Need to have RNAi objects in database
    • Mapping data could be included with the RNAi object or separately.
    • Need to come up with an official schema for storing this data
  • Deciding on making this a one of or something that we do every release
    • Making it for each release is something that would help users as it has come up in many helpdesk tickets over the years (Chris Grove)
    • If we show this data we will need to make sure it is clear to the user that the information was generated in-silico
      • This could be made as a Micro Publication to make sure users use the data correctly
    • Would entail generating a bolus of mappings between RNA and Gene Targets

Two open tickets:

BioCyc-WB Links

  • Report back from follow-up meeting last Thursday with Peter Karp:
    • BioCyc will make available pathway images that WB will display, initially, on gene and molecule pages
    • We'll also have reciprocal links
    • Minutes

Minutes

  • Kimberly decided she would create a Ticket for this
    • Here it is: https://github.com/WormBase/website/issues/8572 Display BioCyc pathway images at WB
      • BioCyc will create a web service for WB to access C. elegans pathway images, then WB will display the pathways on relevant gene and molecule pages

Bob Waterson single cell embryo data

  • Bob asking if interested in displaying the single cell embryo data from their 2019 Science paper in WormBase
  • He has large tables of the tpms per cell type and for the lineage as well as the percent of cells expressing. * He made graphs of these, not interactive
  • Could go in the 'Single cell gene expression graphs' section, where Sibyl put in CenGen Data. https://wormbase.org/species/c_elegans/gene/WBGene00001170#c13--10
  • Can Web Team display the Bob's graphs, too?
  • if we have the data we can generate a similar graph
  • If they offer static images we could bring in as images or the Web Team can display directly on the 'Single cell gene expression graphs' section
  • Daniela to talk to Todd and see what is the best way forward
  • If we get raw data we can display as CenGen, may be able to reuse Sibyl's code
  • Quickly get static images in is #1 priority

Minutes

  • Assuming Sibyl's code for CenGen can be adapted
    • Priority one is to get the images in that we already sent to us (Raymond)
      • Add data (csv files) into a more interactive graph. At first display static data.
      • Start with graphs that have already been generated by Bob
    • First action item is to get data already generated by Bob

Ticket has been generated for this work: https://github.com/WormBase/website/issues/8574 Bob Waterson single cell embryo data #8574

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