GO-CAM Working Group Call 2018-10-23

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Meeting URL

https://stanford.zoom.us/j/976175422

Agenda

Review Action Items from Montreal Meeting

  • Establish a GO-CAM chat room on https://gitter.im/geneontology/home
    • Seth has established a go-annotation chat room on gitter since this can be synced with the go-annotation repo wrt invitations
    • Will use as a way to get more timely feedback and answers to modeling questions
    • Monitor and collate questions for a GO-CAM FAQ
    • Link from Noctua? Graph editor, forms, landing page?
  • Add an FAQ to the Nocuta/GO-CAM documentation
    • Landing page now linked from main Noctua documentation page
    • Noctua documentation page now linked from Annotation home page
  • Intermediate-level GO-CAM camp?
    • When? Where? Level of interest?
  • Documentation for annotation data flow
    • New annotations captured as GO-CAM models
    • Existing annotations added to GO-CAM models

Noctua Roadmap

Modeling Transcription

Key Points

  • Direct vs Indirect
    • Direct: include target using 'has input' relation for both MF and BP
    • Indirect: do not include target on MF and BP
    • Relation between transcription process and activity of target is the same

Next Week's Meeting

  • October 30th - fifth Tuesday, ad hoc meeting, if desired

Minutes

  • On call: Barbara, Bob, Chris, David, Dmitry, Dustin, Edith, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Li, Marie-Claire, Penelope, Petra, Rachael, Rob, Sabrina, Seth, Stacia, Suzi A, Suzi L, Tanya

Review Action Items from Montreal Meeting

  • go-annotation chat room is set up on gitter: https://gitter.im/geneontology/go-annotation
    • it is public and anyone can join
    • we will experiment with this as a forum for getting more immediate feedback on annotation issues
    • gitter can be accessed via a desktop app or the web, but does not work well in Safari (Chrome okay)
  • Landing page for GO-CAM/Noctua FAQs now linked from the Noctua wiki documentation
    • Will begin to populate with questions about using the tool and creating models
  • GO-CAM camp?
    • Will need to gauge level of interest and funds to see if we can schedule this
  • Documentation for annotation flow
    • High priority for understanding the path of Noctua-based annotations (newly created and integrated from existing annotations)

Noctua Roadmap

  • Please review and add comments
  • We will be fleshing this out and working from this over the coming year

Transcription Models

  • Direct regulation of transcription will be captured using a TF activity MF term that is part_of regulation of transcription (could be positive or negative)
  • The input to the MF and BP in this case would be the same and curators would only need to create one instance of that input
  • Separate evidence could still be placed on the relation between the MF and BP to the input, though
  • This way of modeling will produce the expected output for BP in the derived GPAD (i.e. no redundancy in inputs/participants

Meeting Schedule

  • May just have Alliance function calls on the first Tuesday to leave remaining Tuesday calls open for GOC
  • Need to confirm with Nathan if this is okay - Stacia will check with him

Alliance All-Hands Meeting

  • Will schedule some time on the agenda to discuss Noctua and moving Alliance groups to using Noctua for GO curation
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