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Agenda and Minutes
- Present: Bob, Chris, David, Edith, Giulia, Harold, Helen, Karen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Penelope, Sabrina, Seth, Stacia, Stan, Suzi, Tanya
Annotation Calls
- We will meet weekly on Tuesdays at 8am PST.
- Will no longer make the distinction between annotation and GO-CAM/Noctua calls.
Noctua
- Noctua will be updated later today to make the new Noctua form the default version of the form.
- Please let us know if you experience any trouble with Noctua after the update, or have questions on how to use the form.
- Documentation is here: http://wiki.geneontology.org/index.php/Noctua
Annotation Relations
- Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
- Relation to discuss this week:
- 'activated by'
- https://github.com/geneontology/go-annotation/issues/2718
- 'activated by' had been defined as a relation 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, an example is:
- GeneProduct 1 'enables' small molecule binding (GO:0036094) '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)
- Ontology editors could discuss these types of terms and making sure we are consistent with term creation and labels