GO-CAM Working Group Call 2018-11-27
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Agenda
- Meeting URL: https://stanford.zoom.us/j/976175422
Progress Reports
- 2018 progress reports are due Friday, December 14th
- For working groups, folder for 2018 reports, with template, is on the GO's Google drive.
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
- Currently, GPAD files are available here:
- Check with Seth on status of:
- Proposed new (transitional) location for Noctua GO-CAM pick up:
- "noctua_RESOURCE.gpad.gz" in http://snapshot.geneontology.org/products/annotations/
- Example: "noctua_wb.gpad.gz"
- "noctua_RESOURCE.gpad.gz" in http://snapshot.geneontology.org/products/annotations/
Minutes
- 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