WBConfCall 2020.04.02-Agenda and Minutes

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Agenda and Minutes

Adding strain genotype information

  • Having strains with only an ID is not useful, without the genotype
  • Easy to add the genotype information when a curator is reading the paper, and to do it at the same time as request for the ID
  • Not efficient to have to e-mail and then wait for this to be added
  • Where do we fill in the genotype info?
  • Any development beyond the current system will be an additional project
  • We can currently use the free text box, when Hinxton retrieves the objects from the name service, it performs a string match on e.g. genes, Papers, etc..
  • This is suboptimal but is a fix for now
  • Kevin: need to flash out the requirements for the next phase of development (Caltech, Hinxton, Sibyl)
  • Kevin asking what was the need of an extra CGI, Juancarlos explained the reason, i.e. having objects promptly available in the OA
  • Raymond: need for a staging and test environment? Todd: this is in motion
  • How are strains entered in geneace? Genotype is free text, but should follow nomenclature.
  • Paul S: how are molecular changes put in the database? Paul D: via allele sequence submission form, then an html table is created and an ace file is generated. If not enough info is provided, Paul D will look at it manually.
  • Need to come up with a curation tool for molecular changes, need a good workflow to make it efficient

Evidence and Conclusion Ontology in WB

  • In preparation for the new GO file formats, GPAD/GPI 2.0, we'll need to incorporate the Evidence and Conclusion Ontology (ECO) into WB
  • Working on a model for ECO in WB
  • This would replace ?GO_code in the ?GO_annotation model
  • Other models use ?GO_code - do we want to switch them to ?ECO_code at some point as well?

GitHub Tickets

  • Where can i find the upstream and downstream limits for a gene? #7651 and #7652. College assignment
  • Maureen Barr's question about protein coding genes with known function; can this be closed?
    • I responded to Maureen with some of the ideas/thoughts we had when we discussed this on a previous call. I haven't heard back from her, but thought it might be a good idea to keep the ticket open as it raised an interesting issue that might be worthwhile future work for WB. Okay to close, though, if people would prefer that.