WBConfCall 2020.06.18-Agenda and Minutes
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- Is it confirmed? July 10 Citace 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
- Went live yesterday
- 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?
- Email came in on Tuesday, June 16th
- 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)
- She retracted her question now but 2bp-intron is still weird.