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
  • PaulD will be the contact curator for microPublication allele-seq requirements

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 for WS278
  • 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?
  • Ranjana: this will impact disease annotations
  • The entire ECO will be brought in

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.

ZOOM Meeting with Password?

  • To prevent against meeting crashers.
  • People joining by computer will just have an URL to click on
  • Harder to join if you are driving

WS277 upload

  • Caltech is going to upload data tomorrow
  • Are there changes in the transgender class? Chris: not yet, might send a patch to Hinxton