GO-CAM Working Group Call 2018-11-27

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Progress Reports

GO-CAM Relations

causally upstream of, positive effect

  • causally upstream of, positive effect - http://wiki.geneontology.org/index.php/Causally_upstream_of,_positive_effect
    • In the clocka model, the activity of the clocka TF is 'part of' a process that is 'causally upstream of, positive effect' on the activity of its transcriptional target, smad3a
    • Contrast this with the activity of gene products such as a Nodal receptor that phosphorylates smad3a or CBP that acetylates smad3a to enhance its transcription factor activity

Root MFs vs Known MFs

  • When should curators use the root MF in a model vs a known MF?
    • In the clocka model, the smad3a gene is annotated to root MF. Should it be annotated to a known smad3a MF?
    • In doing so, models would be more 'complete', incorporating what is already known and annotated about MFs
    • Using the Noctua form, it is easy to bring in existing annotations
    • Evidence on an assertion will show how the inference is made
    • Curators should use their best judgement about cases where a gene product may have more than one function (e.g. choose a suitable parent term)
    • Updating models as new knowledge is published is imperative
    • Will maintain consistency between our current practice

GO-CAM GPAD - Pipeline


  • On call: David H., Dmitry, Giulia, Harold, Jim, Kevin, Kimberly, Laurent-Philippe, Liz, Marie-Claire, Pascale, Penelope, Petra, Sabrina, Seth, Stacia, Suzi A, Suzi L, Tanya