Agenda and Minutes

Annotation Relations

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
- Going forward, though, the aims are to:
  - 1) model regulatory events in terms of activities enabled by gene products (this implies that we have some knowledge of the regulatory mechanism)
  - 2) capture bona fide regulatory molecules (what is being 'sensed'), but not cofactors such as ions or coenzymes
- For standard annotation, it will typically look like this:
  - GeneProduct 1 'enables' binding (GO:0005488) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
  - GeneProduct 1 'enables' molecular function
- Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296
- Note that, in some cases, we have MF terms that capture what curators may have been trying to capture with 'activated by', e.g. calcium-activated potassium channel activity (GO:0015269)