Annotation Conf. Call 2017-08-08: Difference between revisions
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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) | |||
=== Action Items === | === Action Items === | ||
Revision as of 11:27, 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)
Action Items
- AI: Document the methodologies used to create and analyze slims
- AI: Supply list of GO IDs used for GO slims (make new github ticket)
- Supply ID - Name pairs