WBConfCall 2021.06.17-Agenda and Minutes

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Help Desk

Open tickets:

Phenotype:cortical granule exocytosis variant https://github.com/WormBase/website/issues/8279 - Assigned to Gary Schindelman

I'd like to make a genome-wide graphic like the original 1998 C. elegans genome project paper https://github.com/WormBase/website/issues/8274 - Assigned to Scott Cain, looks like user is happy with Scott's sugestion of using jBrowse next gen

Show DNA_text on WB Construct page https://github.com/WormBase/website/issues/8267 - Assigned to Adam Wright

Agenda and Minutes

WS281 issues

  • Empty assemblies[] in the ASSEMBLIES.WS281.json file
  • discordant feature names in Ace and GFF for (at least some) Tier III species
    • HX will unify the acedb and gff IDs so that the web code will not need to be changed.


CenGen data

  • GitHub #8075: https://github.com/WormBase/website/issues/8075
  • 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

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
  • Can the files be stored on the ftp and the plots be displayed on the expression widget?
  • Bring in data both as pictures and interactive bar plots
  • Decided to put data on FTP. Daniela, Sibyl, Raymond will set up a meeting with Seth to get further insight of raw data and on how to reproduce the plots.
  • no need to remap, will be static connections to the genes provided by CenGen

Gene-Variation Associations

  • Caltech is not getting all of the gene-variation associations from the nightly geneace dump (e.g. some tm variation-gene associations are not in the OA curation tool)
  • If gene-variation associations are/will be made via the VEP pipeline that is part of the build, then we should get this information from each WS release?
  • We'd just like to confirm with Hinxton what the best strategy is
  • Associate WBGenes with 'tm' variations in nightly geneace variations file https://github.com/WormBase/website/issues/8262


IWM 2021

  • WB workshop schedule - Date: Tuesday, June 22, 11:30 am - 1 pm (EDT); 8.30 am - 10 am (PDT); 4.30 pm - 6 pm (BST)

11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase

11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data

12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources

12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline

12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A

Presentations and other meeting info in this folder