Annotation Conf. Call 2017-08-08: Difference between revisions
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= Minutes = | = Minutes = | ||
*On call: David H., Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Penelope, Petra, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Terry, Val | *On call: David H., George, Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Paul T., Penelope, Petra, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Terry, Tom, Val | ||
== Ontology Report == | == Ontology Report == | ||
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***Genes not annotated to any term at all | ***Genes not annotated to any term at all | ||
**Co-annotation can be used to capture information when a combined term in the ontology cannot be made | **Co-annotation can be used to capture information when a combined term in the ontology cannot be made | ||
**Analysis can help determine when there might need to be work done on the ontology (e.g. missing relations) or on the annotations (e.g. cytoplasm annotations -> cytosol annotations) | |||
**Note that in the AGR display, the labels may need to be adapted to be more biologist friendly | |||
**Can we have some outside review of the labels? | |||
=== Action Items === | === Action Items === | ||
*'''AI:''' Document the methodologies used to create and analyze slims | *'''AI:''' Document the methodologies used to create and analyze slims | ||
*'''AI:''' Supply list of GO | *'''AI:''' Supply list of GO ID - Name pairs used for GO slims (new github ticket - https://github.com/geneontology/go-ontology/pull/14031) | ||
** | *'''AI:''' Get feedback from users on GO slim term labels | ||
**Pascale will send out the list | |||
== Signaling Project == | |||
*Wnt - Giulia, Helen, Kimberly | |||
**[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis] | |||
**[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets] | |||
**Re-opened ticket on receptor agonist activity | |||
**Consolidating other observations to create additional tickets | |||
*MAPK - David H., Sabrina | |||
**Examining genes for MAPK pathway +/- MF support | |||
**Looking at gene products potentially upstream/downstream | |||
*Ca2+ Signaling - Penelope | |||
**Still needs an ontology editor | |||
*GPCR - Pascale, Petra | |||
**Have downloaded annotations, but still need to review them | |||
**Have created a generic GO-CAM model | |||
***A few templates already existed - link to model 0000200, 0000466, 0000486 | |||
***Is the heterotrimeric G protein cycle term needed? | |||
***How much detail should be included about the functions of the members of the pathway? | |||
***If there is more than one way to represent a pathway, how should we choose which way to annotate? | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 12:05, 8 August 2017
Meeting URL
Agenda
Ontology Report
- SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
- GOC slim ticket https://github.com/geneontology/go-ontology/issues/13996
- Modification to AGR slim
- Confirm that all AGR member groups are okay with current version of GO AGR slim
Signaling Project
- Update on progress to date, github tickets
- Wnt - Giulia, Helen, Kimberly
- MAPK - David H. and Sabrina
- Examining gene products annotated to the process with no experimental support for known MFs
- Thinking about how to define the beginning and parts of the pathway
- Ca2+ Signaling
- Fertilization - Penelope
- GPCR - Pascale, Petra
- Some ontology tickets have been addressed
- Needs global annotation review
- Needs GO-CAM model
- Reminder - discussion on specific github tickets, not on project page
Minutes
- On call: David H., George, Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Paul T., Penelope, Petra, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Terry, Tom, Val
Ontology Report
Check Annotations
- SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
- Annotations to SUMO protease terms may be able to be deepened to one of the two more specific SUMO protease terms (endopeptidase or isopeptidase)
- Gene products annotated are listed on the github ticket
GO Slims
- GOC slim ticket https://github.com/geneontology/go-ontology/issues/13996
- Mary will use her algorithmic method, but the output slim will need review from GOC member groups
- Val's matrix tool can be a good tool for checking redundancy in the slim
- Can also help address whether the chosen terms are too high level to be useful
- Modification to AGR slim
- Confirm that all AGR member groups are okay with current version of GO AGR slim
- Doug had suggested including additional bins for:
- Genes not mapped to any term in the slim (other)
- It can be very difficult to try to map all genes to a slim term - you want to have biologically meaningful term selection without including terms that are too high level or too specific
- http://pombase2.bioinformatics.nz/browse-curation/fission-yeast-go-slim-terms
- For an example of how “other” bins look in ribbons see http://beta.flybase.org/reports/FBgn0011327.html
- Genes not annotated to any term at all
- Genes not mapped to any term in the slim (other)
- Co-annotation can be used to capture information when a combined term in the ontology cannot be made
- Analysis can help determine when there might need to be work done on the ontology (e.g. missing relations) or on the annotations (e.g. cytoplasm annotations -> cytosol annotations)
- Note that in the AGR display, the labels may need to be adapted to be more biologist friendly
- Can we have some outside review of the labels?
Action Items
- AI: Document the methodologies used to create and analyze slims
- AI: Supply list of GO ID - Name pairs used for GO slims (new github ticket - https://github.com/geneontology/go-ontology/pull/14031)
- AI: Get feedback from users on GO slim term labels
- Pascale will send out the list
Signaling Project
- Wnt - Giulia, Helen, Kimberly
- Google spreadsheet with annotation, ontology analysis
- Google doc for crystallizing github tickets
- Re-opened ticket on receptor agonist activity
- Consolidating other observations to create additional tickets
- MAPK - David H., Sabrina
- Examining genes for MAPK pathway +/- MF support
- Looking at gene products potentially upstream/downstream
- Ca2+ Signaling - Penelope
- Still needs an ontology editor
- GPCR - Pascale, Petra
- Have downloaded annotations, but still need to review them
- Have created a generic GO-CAM model
- A few templates already existed - link to model 0000200, 0000466, 0000486
- Is the heterotrimeric G protein cycle term needed?
- How much detail should be included about the functions of the members of the pathway?
- If there is more than one way to represent a pathway, how should we choose which way to annotate?