Projects update meeting 2023-01-25

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Attendees

  • Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
  • Present: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
  • Regrets: David

Announcements

GOC meeting

will be held immediately after Biocuration, in Padua, Italy (Thursday April 27th to Saturday April 29th)

  • How many registrees do we have? We need to provide a ~final number at the signature of the contract
    • Suzi: 5 registrees -- sent another email
    • Estimated registration fee: 275 €; 300 USD


  • To confirm
    • 3-1/2 days: Thurs, Fri, Sat, Sun AM
    • 3 lunches (Thurs, Fri, Sat)
    • 5 coffee breaks (2 Thurs, 1 Fri, 2 Sat)
    • We need to pay some fraction in advance: something like 40% 2 months before, 30-40% 1 month before, the rest 7 days before (NH) or 7 days after (Best Western) the meeting: Can USC pay by these dates?
  • Hotel options: NH or Best western - within 200 m of each other, ~15 minutes from ISB venue, 25 minutes from city center

GO progress report HG012212 year 1 progress report (Apr2022 to Mar 2023)

Projects reviews

https://github.com/orgs/geneontology/projects/108/views/3

  • For project reviews, please let us know
    • whether there are blocking issues
    • if the scope has changed (new tickets added)
    • delivery/next review date (keeping in mind we'd like each project to last max 2 months)
  • This week's projects to review:
    • Relations to link MFs - Kimberly
      • Need to discuss conditional replacements in GO-CAM models
        • At its simplest, we can substitute all positively/negatively regulates causal relations between MFs with directly positively/negatively regulates
        • However, we know that will generate some incorrect models where, for example, the regulation is indirect according to our new annotation guidelines
        • Can we thus also correct (at least some of) the indirect regulation relations? What would the best order of operations be?
        • For example, there are 138 models that use the MF DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228) - these may not all be causal, but it'd be great to fix the ones we can
          • We could replace positively regulates with indirectly positively regulates and they would now be correct
          • We could also replace causally upstream of, positive effect with indirectly positively regulates
        • Another example, MF mRNA base-pairing translational repressor activity (GO:1903231) - negatively regulates or causally upstream of, negative effect -> indirectly negatively regulates
      • See draft tsv
      • Perhaps the initial broad MF-MF replacement would just be a one-off and going forward we would encourage compliance by use of the VPE and error reports/QC checks
      • Have asked Tremayne to PR fix for handling old relations in the VPE pop-up to dev and Jim to investigate the missing label for indirectly positively regulates in the VPE pop-up (I don't think either of these are blocking, especially if we implement the broader replacements computationally)
  • WB Noctua migration:
    • New file from Alex with errors fixed
    • QCing right now

Project management kaban https://github.com/orgs/geneontology/projects/108/views/1

Proposed priorities for the next 6 months

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