GO-CAM Conference Call - 2019-01-15: Difference between revisions
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= Meeting URL = | = Meeting URL = | ||
* | *Please consult the GO calendar | ||
= Agenda = | = Agenda = | ||
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*On call: Barbara, Chris, David, Dustin, Elena, Giulia, Harold, Helen, Kimberly, Laurent-Philippe, Marie-Claire, Petra, Rob, Ruth, Sabrina, Seth, Stacia, Suzi A | *On call: Barbara, Chris, David, Dustin, Edith, Elena, Giulia, Harold, Helen, Kevin M, Kimberly, Laurent-Philippe, Marie-Claire, Paul T., Petra, Rob, Ruth, Sabrina, Seth, Stacia, Suzi A | ||
*Import of whole genomes | |||
**David, Kimberly, and the software team will have a f2f meeting to work on importing the first two whole genome's worth of annotation for WormBase and MGI | |||
**Will report back on a future call - decisions made, any problems that arose, etc. | |||
**For converting annotation extensions, Paul T. and Dustin have done some preliminary work which groups should look at on the corresponding wiki page: | |||
***http://wiki.geneontology.org/index.php/Extensions2GO-CAM | |||
***has_regulation_target is one of the most commonly used extension relations and it is not used in GO-CAM | |||
****Its translation may depend on the particular GO term with which it was used. | |||
**Model manipulation will likely be key for dealing with whole genome's worth of annotation imports and we will need to gather explicit requirements for that | |||
*Continued discussion of modeling questions | |||
**Will spend time this year discussing annotation of protein complexes, their members, and associated activities | |||
**Will also discussion 'instance' level representation of biological processes and implications for workflow | |||
***[https://drive.google.com/drive/folders/119pVRxuGZK9keJaVDZk2Z4kzNoysuQwZ Google folder for capturing examples for discussion of instance-level representation] | |||
**Models involving, or based on experiments in, multiple species need to be discussed, as well | |||
*Import of Reactome pathways | |||
**Smaller working group will be examining import of Reactome pathways into GO-CAMs | |||
**Specific pathways have been chosen based on preliminary work already done, e.g. glycolysis and signaling, ER-UPR | |||
**This work should, and already has been, very informative for how we model things in GO-CAM | |||
**Reactome imports also raises issues about model size and delineating and linking smaller models that are causally related | |||
*GO-CAM display | |||
**Petra has shown some of the dicty community GO-CAM models | |||
**Reaction was positive, but we need to spend more time working on various display options, making people aware of what APIs already exist for grabbing data for display, etc. | |||
**Whole genome import is currently the top priority, but intuitive, user friendly display of models is very important and will be the subject of future work | |||
[[Category: GO-CAM]] | |||
[[Category: |
Latest revision as of 06:18, 12 April 2019
Meeting URL
- Please consult the GO calendar
Agenda
- From 2019-01-07 annotation conference call:
- Import of whole genomes
- Working meeting at Berkeley the end of this month
- WormBase and MGI will be the first genome annotation sets to be imported
- gp2term relations
- evidence and annotation extensions
- search, display, editing
- gpad output
- overall data flow
- documentation
- Continued discussion of modeling questions
- Annotation of protein complexes and their respective members
- When to annotate to a complex vs making each individual MF just 'part of' the same process?
- Nuclear Pores Regulate Muscle Development and Maintenance by Assembling a Localized Mef2C Complex
- Instance-level representation
- When to annotate to the same 'instance' of a biological process vs different 'instances'?
- Implications for curator workflow
- Modeling from multiple species
- Creating a model for one species when the evidence derives from experiments in multiple species
- Creating models for processes that involve more than one species
- Annotation of protein complexes and their respective members
- Import of Reactome pathways
- Glycolysis
- MAPK
- BMP
- Wnt
- ER-UPR
- GPI synthesis
- Size limitations and delineation of 'models'
- How to 'stitch' or connect large models in a consistent manner that allows us to represent dependencies (upstream, downstream) in a biologically meaningful way that is also computationally amenable
- Model manipulation
- Generation and use of templates
- Merging models
- Copying and/or re-using annotations
- Import of whole genomes
Minutes
- On call: Barbara, Chris, David, Dustin, Edith, Elena, Giulia, Harold, Helen, Kevin M, Kimberly, Laurent-Philippe, Marie-Claire, Paul T., Petra, Rob, Ruth, Sabrina, Seth, Stacia, Suzi A
- Import of whole genomes
- David, Kimberly, and the software team will have a f2f meeting to work on importing the first two whole genome's worth of annotation for WormBase and MGI
- Will report back on a future call - decisions made, any problems that arose, etc.
- For converting annotation extensions, Paul T. and Dustin have done some preliminary work which groups should look at on the corresponding wiki page:
- http://wiki.geneontology.org/index.php/Extensions2GO-CAM
- has_regulation_target is one of the most commonly used extension relations and it is not used in GO-CAM
- Its translation may depend on the particular GO term with which it was used.
- Model manipulation will likely be key for dealing with whole genome's worth of annotation imports and we will need to gather explicit requirements for that
- Continued discussion of modeling questions
- Will spend time this year discussing annotation of protein complexes, their members, and associated activities
- Will also discussion 'instance' level representation of biological processes and implications for workflow
- Models involving, or based on experiments in, multiple species need to be discussed, as well
- Import of Reactome pathways
- Smaller working group will be examining import of Reactome pathways into GO-CAMs
- Specific pathways have been chosen based on preliminary work already done, e.g. glycolysis and signaling, ER-UPR
- This work should, and already has been, very informative for how we model things in GO-CAM
- Reactome imports also raises issues about model size and delineating and linking smaller models that are causally related
- GO-CAM display
- Petra has shown some of the dicty community GO-CAM models
- Reaction was positive, but we need to spend more time working on various display options, making people aware of what APIs already exist for grabbing data for display, etc.
- Whole genome import is currently the top priority, but intuitive, user friendly display of models is very important and will be the subject of future work