Annotation Conf. Call 2020-01-28: Difference between revisions
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**'activated by' had been used to identify a chemical substance that increases the activity of the gene product | **'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: | **Going forward, though, the aims are to: | ||
*** | ***model regulatory events in terms of activities enabled by gene products (this implies that we have some knowledge of the regulatory mechanism) | ||
*** | ***capture bona fide regulatory molecules (what is being 'sensed'), but not cofactors such as ions or coenzymes | ||
****experiments that determine an enzyme's ion specificity, for example, would not be annotated | |||
**For standard annotation, it will typically look like this: | **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' binding (GO:0005488) 'has_input' (some chemical), 'directly_positively_regulates' molecular function |
Revision as of 18:12, 27 January 2020
Agenda and Minutes
- Present:
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:
- model regulatory events in terms of activities enabled by gene products (this implies that we have some knowledge of the regulatory mechanism)
- capture bona fide regulatory molecules (what is being 'sensed'), but not cofactors such as ions or coenzymes
- experiments that determine an enzyme's ion specificity, for example, would not be annotated
- 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)