Revision as of 17:54, 27 January 2020

Agenda and Minutes

Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
Relations to discuss this week:
- 'activated by'
- https://github.com/geneontology/go-annotation/issues/2718
- 'activated by' had been used to identify a chemical substance that increases the activity of the gene product.
- We would like to instead model this as:
  - GeneProduct 1 'enables' binding (GO:0005488) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
  - GeneProduct 1 'enables' molecular function
- The aims are to:
  - 1) model regulatory events in terms of activities enabled by gene products (this implies that we have knowledge of the regulatory mechanism)
  - 2) capture bona fide regulatory molecules, but not cofactors such as ions or coenzymes
- Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296

@@ Line 11: / Line 11: @@
 ***GeneProduct 1 'enables' binding (GO:0005488) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
 ***GeneProduct 1 'enables' molecular function
-**The aims are to: 1) model regulatory events in terms of activities enabled by gene products, and 2) capture bona fide regulatory molecules, but not cofactors such as ions or coenzymes.
+**The aims are to:
+***1) model regulatory events in terms of activities enabled by gene products (this implies that we have knowledge of the regulatory mechanism)
+***2) capture bona fide regulatory molecules, but not cofactors such as ions or coenzymes
 **Sample GO-CAM model:  http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296