GO-CAM Working Group Call 2018-09-25
Meeting URL
https://stanford.zoom.us/j/976175422
Agenda
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'
Relations between MF and Input(s)
- How did this discussion start?
- http://noctua.geneontology.org/editor/graph/gomodel:5a5fc23a00000137
- 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:
- Enzyme-substrate
- Enzymatic modification of a substrate
- Enzyme-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
Relations between BPs and Input(s)
- Adding the same input to an MF and BP of which that MF is a part
- Is this necessary? Does is add anything to the model?
- The resulting AEs for the process then have two references to the input, one captured with the asserted 'has input' and the other with the inferred 'has participant'.
Minutes
- On call: