Difference between revisions of "WBConfCall 2020.06.18-Agenda and Minutes"

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** Email came in on Tuesday, June 16th
 
** Email came in on Tuesday, June 16th
 
** GitHub ticket: https://github.com/WormBase/website/issues/7747
 
** GitHub ticket: https://github.com/WormBase/website/issues/7747
 +
** Paul D has responded and is looking into
 
* 2 bp intron in Cbr-hipr-1 (helpdesk email from Marie-Anne Felix)
 
* 2 bp intron in Cbr-hipr-1 (helpdesk email from Marie-Anne Felix)
 
**https://wormbase.org/species/c_briggsae/transcript/CBG15345a.1#06--10
 
**https://wormbase.org/species/c_briggsae/transcript/CBG15345a.1#06--10
 
** She retracted her question now but 2bp-intron is still weird.
 
** She retracted her question now but 2bp-intron is still weird.

Revision as of 14:48, 18 June 2020

Agenda

WS278

  • Is it confirmed? July 10 Citaace upload to Hinxton.

Testing data for WS278 model changes

  • All disease data files passed Caltech and Hinxton testing
  • New genotype data file passed testing

AFP entity extraction

  • Strain to paper association. Does every strain mentioned in the paper need to be connected? e.g. N2, OP50.. What about alleles and transgenes used as reagents?
  • Species association. For species we are using a threshold that is quite high (10 mentions) that gets rid of false positives (e.g. anti-mouse, anti-rabbit antibodies, etc..). We have some papers, though that mention other nematodes with a low count (especially for phylogenetic studies) but might be worth to record in WB. Would it be worth to set up a separate pipeline that identifies those papers and populates a reference widget in WB for a given species (e.g. brenneri, japonica, pacificus, ..)?

Help Desk

  • Subject line: WormBase - Study on the Audience of Scientific Databases and Data Repositories
    • Email came in Monday, June 8th
    • Do we want to share WormBase "audience" data for research project?
  • Question about Cre-oac-31 and Cre-oac-42; seem to have disappeared?
  • 2 bp intron in Cbr-hipr-1 (helpdesk email from Marie-Anne Felix)