Difference between revisions of "LEGO May 2, 2016"
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Revision as of 10:16, 2 May 2016
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?
- More video tutorials? (Stacia)
current tutorials on Vimeo: https://vimeo.com/channels/Noctua
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
- On call: Chris, David H., Heiko, Kimberly, Stacia, Suzi
- Software Updates - none this week
- GAF/GPAD outputs
- We discussed the Wnt secretion model and how to create a model that will allow for the appropriate causally_upstream_of and regulates relations to be recovered in the GAF/GPAD output.
- When creating causally_upstream_of or regulates relations, how and where to include the evidence?
- Evidence for an activity may be different from evidence of the effect of that activity on a downstream process. We'll need to explicitly add the relations and evidences for activities and downstream processes to have them correctly represented in the model and resulting output files.
- We also discussed the extent of what upstream processes might be included in a given model and to what extent known specificity plays into the decision to include commonly used cellular processes.
- AI: Need to work out the qualifier proposal.
- Stacia and Kevin at SGD can help produce new training videos for the basic functionality of Noctua, including login, creating an annoton, adding relations, adding evidence, etc.