LEGO May 2, 2016
Bluejeans
https://bluejeans.com/969313231
Agenda
Software Updates
GAF/GPAD
Determining the Extent of Upstream/Downstream to Capture in GAF/GPAD
- For an illustration, see: http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000082
- Fatty acylation of Wnt is required for its secretion
- Currently, worm, fly, fish, mouse, and human acyltransferases of the porcupine family are annotated to Wnt protein secretion or some variant (direct or regulation) of Wnt signaling pathway
- The current GAF/GPAD output only includes, as an annotation extension, the immediate downstream process which in the illustrative model is 'Golgi to plasma membrane transport'
- Is there/could there be a mechanism whereby curators indicate which annotons to include as causally_upstream of GAF/GPAD output for a given model?
- What do we still need to get GAFs that can be used?
- In the meantime we should just go for the default of including everything. It is easier to prune annotations that to add them in a second step later. This means that everything causally downstream of a gene's function will be annotated, but I don't think that it is that much different from the historical way of doing annotation.
- We need to find a way to indicate attribution. I suggest that we use GO-curator xref-Noctua (dph-Noctua) in column 15.
- Related to this, can new ontology terms be automatically generated from a model and curators given the option to add them to the ontology when they save their models?
Documentation
- More video tutorials? (Stacia)
Models Discussion
cdc2 - Continuing Discussion from 2016-04-25
- How to correctly represent regulatory activities and the corresponding entities?
- See: http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000003