GO-CAM Conference Call - 2019-05-21: Difference between revisions
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= Minutes = | = Minutes = | ||
*On call: Dmitry, Dustin, Edith, Elena, Giulia, Harold, Helen, Jim, Karen, Kevin M, Kimberly, Laurent-Philippe, Li, Marie-Claire, Monica, Pascale, Petra, Sabrina, Seth, Stacia, Suzi A, Tanya | *On call: Dmitry, Dustin, Edith, Elena, Giulia, Harold, Helen, Jim B, Karen C, Kevin M, Kimberly, Laurent-Philippe, Li, Marie-Claire, Monica, Pascale, Petra, Sabrina, Seth, Stacia, Suzi A, Tanya | ||
== Annotation Imports == | |||
* David and KImberly assessing annotations to BP 'regulation of molecular function' and children that use 'has_regulation_target' extension to see if these could all be modeled just with MFs | |||
* Continue to check new AE models as they come on board | |||
== Modeling Questions == | |||
* caspy2/caspb zebrafish model | |||
** Each MF, including binding terms, need to be annotated with an enabled_by relation when the entity is known | |||
* caspy2/caspb zebrafish and ire1-er-upr c. elegans models | |||
* We discussed the utility of MF and BP terms related to multimerization in both GO-CAM models and conventional annotation | |||
* Multimerization can be a necessary step before execution of an MF, e.g. receptor tyrosine kinases | |||
* However, are annotations to multimerization MF and BP terms critical for GO-CAM models? Do they add anything on their own as conventional annotations? | |||
* Molecular-level details may be interesting to biologists that want to know every step in a pathway, but this brings challenges for curation and display | |||
* Is regulation of multimerization more important to capture? | |||
* For curation, do we want to capture these experimental observations, even if it's not yet clear how they fit into the overall biological process | |||
** Capturing all information while reading a paper is more efficient than trying to go back and make annotations from previously curated papers | |||
* For display, it could be useful to have different views of a model (one with the details, one with just the essential, or main, functions) and allow users to toggle between them | |||
** We would want to have specifications for what details would be hidden | |||
* We should continue this discussion since it impacts curation decisions more broadly | |||
[[Category: GO-CAM]] | [[Category: GO-CAM]] |
Latest revision as of 14:19, 21 May 2019
Call Information
- See GO's Google calendar for Zoom URL
- email Kimberly if you need access to the GO's Google calendar
Agenda
Annotation Imports
- Status update on MGI and WB annotation imports
- Implemented imports of With/From
- Re-visiting the rule for modeling BP 'regulation of MF' with has_regulation_target extension
- Additional annotation extensions coming on board
- Track issues on github/gocamgen
Modeling Questions
- From Sabrina on go-annotation gitter:
- "caspy2 binds directly to lipopolysaccharide, resulting in caspy2 oligomerization, which is critical for pyroptosis" ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076302 PMID:30076291})
- I started a GOCAM model, but I am not sure it is correct
- Summary figure from paper
- Related question on modeling activities that influence dimerization state of another protein
- Role of heat shock proteins in initiating C. elegans IRE1-ER UPR
- See: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423427/figure/F3/
Minutes
- On call: Dmitry, Dustin, Edith, Elena, Giulia, Harold, Helen, Jim B, Karen C, Kevin M, Kimberly, Laurent-Philippe, Li, Marie-Claire, Monica, Pascale, Petra, Sabrina, Seth, Stacia, Suzi A, Tanya
Annotation Imports
- David and KImberly assessing annotations to BP 'regulation of molecular function' and children that use 'has_regulation_target' extension to see if these could all be modeled just with MFs
- Continue to check new AE models as they come on board
Modeling Questions
- caspy2/caspb zebrafish model
- Each MF, including binding terms, need to be annotated with an enabled_by relation when the entity is known
- caspy2/caspb zebrafish and ire1-er-upr c. elegans models
- We discussed the utility of MF and BP terms related to multimerization in both GO-CAM models and conventional annotation
- Multimerization can be a necessary step before execution of an MF, e.g. receptor tyrosine kinases
- However, are annotations to multimerization MF and BP terms critical for GO-CAM models? Do they add anything on their own as conventional annotations?
- Molecular-level details may be interesting to biologists that want to know every step in a pathway, but this brings challenges for curation and display
- Is regulation of multimerization more important to capture?
- For curation, do we want to capture these experimental observations, even if it's not yet clear how they fit into the overall biological process
- Capturing all information while reading a paper is more efficient than trying to go back and make annotations from previously curated papers
- For display, it could be useful to have different views of a model (one with the details, one with just the essential, or main, functions) and allow users to toggle between them
- We would want to have specifications for what details would be hidden
- We should continue this discussion since it impacts curation decisions more broadly