WBConfCall 2018.03.15-Agenda and Minutes

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Importing Undiagnosed Diseases Network (UDN) worm data into WormBase

  • PI in contact: Andy Golden; This is pre-publication data, but my understanding is that we are taking this in, so this is one of the exceptions
  • Initially thought it would be textual data that would go into disease model curation, but really involves other data types such as Variation, Strain, Phenotype, Protein amino acid sequence changes, etc.
  • Example, for amino acid sequence change (from Kevin): include the UniProt protein entry that they used, and track this forward with future versions of the assembly and gene set
  • So looks like we want to integrate the data across these datatypes, in a more organic way, not just textual information, so we will need to co-ordinate between the different data curators
  • When the data is eventually published we will need to make sure everything matches up (something that Chris G. was concerned about)


Alliance working group project plans

  • Due Friday (tomorrow) or Monday
  • Will help Alliance project over long term

Undiagnosed Diseases Network (UDN)

  • Consortium of clinicians and basic researchers
  • Andy Golden: started making human disease mutations in worms
    • Have human disease, mutant change in human protein, corresponding worm mutation and phenotype
    • Wants to put the data into WormBase (prepublication for now)
  • Ranjana and Kevin met with Andy
    • Until we have fancy variation tool, we will pull the basic data into WormBase: phenotypes, allele sequence, etc. possibly as text or basic annotations
  • Group has generated alignments between human and worm proteins (using UniProt proteins)
  • Currently WormBase only has worm mutations/variations not human
    • Would WB really want/need to pull in human variants from ClinVar, dbSNP, etc.?
  • Question: who is going to develop the display (WB? Alliance?)
  • WB will focus on what is most relevant to WB for now; let Alliance handle more generic display (for all Alliance MOs)
  • UDN will produce some micropublications
  • Strains are (or will be) publicly available
  • Can start importing data for WS266
  • Is there anything in the WB data model to pull all the related data together?
    • Disease model annotations?
    • We may want to make connections between the worm mutation and the human variation
    • Ranjana has some proposed model changes to accommodate changes
  • Sibyl will send around link to ortholog variation comparison tool prototype

HTTP vs HTTPS issues

  • Some services break if not at the correct http
  • What needs to be done? Todd: not much; will discuss