GO-CAM Working Group Call 2018-09-25
From GO Wiki
Evidence Codes in Noctua
- Decision: leave evidence codes as is in Noctua
- Will we continue to use full ECO
- Autocomplete searches perform best when searching on first word in term label, e.g. 'direct' or 'mutant'
- Modeling when regulation of transcription is direct vs indirect (or unknown)
- Add input to both the transcription factor activity and the positive (or negative) regulation of transcription process
- Use the 'has input' relation
- Connect the positive (or negative) regulation of transcription process to the function of the affected gene using the 'casually upstream of, positive (or negative) effect'
- GPAD output currently exports both to the BP (one asserted, one inferred), but we want to filter the GPAD output to only export the most granular relation and value
- See: https://github.com/geneontology/minerva/issues/205
indirect or Unknown Regulation
- In this case, do not add an input to the MF or BP, but use the same causal relation, 'causally upstream of, positive (or negative) effect', between the regulation of transcription process term and the function of the gene whose activity is affected
Annotation Review for 'has input' vs 'has direct input'
- We were reviewing a transcription model and discussing how/where to capture inputs of MFs and BPs.
- 'has input' vs 'has direct input'
- In GO-CAM models, we are using 'has input' for capturing the objects of MFs
- This is different from conventional annotation where curators sometimes made a distinction between 'has direct input' and 'has input'
- Proposal: replace 'has direct input' with 'has inpu't; obsolete 'has direct input'
- Need to review has_input annotations to remove any extensions that are inconsistent with GO-CAM usage, i.e. an indirect or unknown proximity for an input
- Seth retrieved, as of 2018-07-31, all MF annotations that use has_input in annotation extensions.
- Use cases to discuss:
- Enzymatic modification of a substrate
- 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
- On call: Chris G., Chris M, Dustin, Edith, Kevin M, Kimberly, Laurent-Philippe, Li, Liz, Marie-Claire, Pascale, Paul T, Penelope, Petra, Rob, Ruth, Sabrina, Seth, Stacia, Stan, Suzi A, Tanya