WBConfCall 2020.12.17-Agenda and Minutes

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Help Desk



  • CeNGEN
    • Will talk in January for integration into WormBase: who should be on that call?
      • Eduardo, Raymond, Todd, Chris
    • Eduardo has several ideas about how to integrate and display
      • Has slides (for Alliance) with a breakdown of technology over time, species represented (mostly human and mouse)
      • First C. elegans dataset in 2017; another in 2019 with re-annotation of 2017 dataset
      • scRNA-seq data sets are in a big sparse matrix
      • Data in raw FASTQ file --> read alignments --> unfiltered matrix --> barcode filtering --> filtered matrix
      • Data deposited usually at SRA and ENA, but often not raw data, usually the already filtered matrix (sometimes even more processed than that)
      • Human Cell Atlas Data Portal (data.humacellatlas.org) (only human and mouse; not interested in other species)
      • COVID19 cell atlas (covid19cellatlas.org)
      • CellXGene (https://cellxgene.cziscience.com/)
      • Should be analyzing differential gene expression (but not using a t-test)
    • What about the EBI gene expression atlas (gxa): https://www.ebi.ac.uk/gxa/sc/home
      • FlyBase already collaborating with
      • Maybe we can use the tools/infrastructure that EBI GXA has; we could curate into their platform and we can build off of what the GXA has
      • http://europepmc.org/article/MED/31665515
  • Alliance documentation of WormBase data types to pull in
    • Todd has built a document based on Doug Howe's file
    • Todd will share his file
    • Kevin H: if we are pulling everything (of current importance) over to the Alliance in 2 years, we'll need to incorporate pipelines that run during or after our build pipelines
    • We can start with Todd's document and build off of that (keeping a centrally located file)
    • To what extent are some of our data available elsewhere? Maybe making it less crucial that we port it over in the short term (users can still get it from somewhere else)
    • Changed interface will likely be jarring to users
  • WormBase Social Hour
    • Tomorrow, Friday, at 12pm Pacific, 3pm Eastern, 8pm UK
    • Kevin will send the Spatial Chat link to staff@wormbase.org
  • WS280 build
    • Any big new datasets to keep an eye on?
    • Request for release notes content; what do we want to highlight?