GO-CAM Working Group Call 2018-08-21

Meeting URL

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

Agenda

GO Annotation Meetings

• Tuesdays at 8am PDT
• Meeting schedule:
  • 1st Tuesday: Alliance Gene Function
  • 2nd Tuesday: GO Consortium
  • 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
  • 4th Tuesday: GO-CAM Working Group
  • 5th Tuesday: ad hoc, as needed
• One Zoom URL for all - https://stanford.zoom.us/j/976175422

Modeling Transcription in GO-CAM

• Sabrina - PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.'

Relations between Transcription Factor MFs and Regulation of Transcription BPs

• Transcription factor activity is 'part_of' regulation of transcription
• This is consistent with the relations in the ontology and produces the correct annotations in the GPAD output file
• A consequence of this is that any regulation terms needed for annotation will have to be instantiated in the ontology
• This principle will be applied more broadly, i.e. if an entity plays a regulatory role in a process, its MF is 'part_of' some regulation of BP

Relations between MF and Input(s)

• has_input vs has_direct_input
• Is there a meaningful distinction between these two relations for MF? What are we really trying to capture with MF inputs?
• Proposal: review MF annotations using has_input
  • Relations Ontology working group (broader than just GO) that is also considering how to model participants in an MF and documentation of has_input and child relations
• Right now, no changes to GO-CAM models (will continue to use has_input)

Direct vs Unknown Mechanism of Regulation

Capturing Unknown Mechanism of Regulation

• If it is not known if the TF directly regulates the expression of a gene, then the input for the TF activity is left blank.
  • In this case, however, it is okay to use evidence from another experiment that might have shown different context (i.e. a different gene was regulated) as supporting evidence for the TF activity.
• The curator can model the unknown mechanism of regulation by saying that the TF is part_of regulation of transcription that is causally_upstream_of_or_within the positive or negative regulation of transcription that ultimately controls the expression of the gene. The gene is then added as 'has input' to the most distal transcriptional regulatory process.

Relations between BP and input(s)

• Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD

Relations between BP and MF of transcriptional target

• causally upstream of, positive effect
• causally upstream of, negative effect

Root Node vs Existing Molecular Functions

• Curators should always try to construct models using the known MF of a gene product, even if that MF was not specifically demonstrated in the paper they are annotating.
• Associated evidence for that MF will always point back to the paper in which the MF was interrogated.
• Creating models in this way will allow us to build on existing knowledge to create the most comprehensive and up-to-date model for a given BP.
• Proposal: if a gene product has more than one MF, curators should use either: 1) experimental data that supports the selection of one function vs another, 2) the common parent of the two functions, or 3) the biological context of the annotated process to select the most appropriate function(s) for that gene product.
  • Examples: beta-catenin and PDIA6

Minutes

• On call: Bob, Chris, David, Dustin, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Laurent-Philippe, Marie-Claire, Pascale, Penelope, Ruth, Sabrina, Seth, Stacia, Suzi A, Suzi L,