Annotation Conf. Call 2020-01-28: Difference between revisions
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= Agenda and Minutes = | = Agenda and Minutes = | ||
*Present: | *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 == | == Annotation Relations == | ||
*Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible | *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' | **'activated by' | ||
**https://github.com/geneontology/go-annotation/issues/2718 | **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 | **'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: | ||
***GeneProduct 1 'enables' binding (GO: | ***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 | ***GeneProduct 1 'enables' molecular function | ||
**Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296 | **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 | |||
*Much discussion on the sample GO-CAM model for annotating the effects of small molecules on the activity of gene products. | |||
*Some of the key issues raised and possible actions: | |||
**Use of 'small molecule binding' or child terms for annotation | |||
***This has been an outstanding issue in GO for some time, but looking at the estrogen receptor model brings it to the forefront again | |||
***We need guidelines on when curators should capture these binding annotations | |||
***If the binding is annotated, then we also need guidelines on when curators should request new pre-composed terms vs when they should annotate to a parent binding term and use the 'has input' extension to capture the actual small molecule being bound | |||
***The ontology editors will discuss this issue and get back to curators with a decision | |||
Latest revision as of 16:59, 29 January 2020
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
- Much discussion on the sample GO-CAM model for annotating the effects of small molecules on the activity of gene products.
- Some of the key issues raised and possible actions:
- Use of 'small molecule binding' or child terms for annotation
- This has been an outstanding issue in GO for some time, but looking at the estrogen receptor model brings it to the forefront again
- We need guidelines on when curators should capture these binding annotations
- If the binding is annotated, then we also need guidelines on when curators should request new pre-composed terms vs when they should annotate to a parent binding term and use the 'has input' extension to capture the actual small molecule being bound
- The ontology editors will discuss this issue and get back to curators with a decision
- Use of 'small molecule binding' or child terms for annotation