WBConfCall 2020.06.18-Agenda and Minutes

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  • 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
  • ECO_term file and GO_annotation files also 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?
    • For strains coming from the AFP pipeline we discussed a potential automated workflow yesterday (Caltech/Hinxton)
    • Note that for gene-paper associations, we try to only associate genes that are studied in some way and not genes used as reagents, e.g. genetic mapping, tissue-specific promoters.
  • 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, ..)?
    • We would need to update the ?Species model to include references.
    • We also associate non-nematode species with papers. It would be nice to include those, as well, especially for pathogens used in C. elegans host-pathogen studies for which we're otherwise not doing much curation.

microPublication in PMC as of yesterday

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)