Difference between revisions of "LEGO May 2, 2016"

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(GAF/GPAD)
(Determining the Extent of Upstream/Downstream to Capture in GAF/GPAD)
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* What do we still need to get GAFs that can be used?
 
* 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.
 
** 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 dph-Noctua in column 15.
+
** 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?
 
*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?
  

Revision as of 07:40, 2 May 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


Minutes