Annotation Conf. Call 2017-08-22: Difference between revisions
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****Wnts | ****Wnts | ||
*****Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but generally an underused term | *****Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but generally an underused term | ||
***** | *****Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common | ||
******Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology | ******Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology | ||
*******Multiple frizzleds exist, but we only have a separate term for frizzled-2; 10 mammalian frizzleds, 2 (?) Drosophila frizzleds, 4 C. elegans frizzleds | *******Multiple frizzleds exist, but we only have a separate term for frizzled-2; 10 mammalian frizzleds, 2 (?) Drosophila frizzleds, 4 C. elegans frizzleds | ||
*******Only 8 experimental annotations to Frizzled-2 binding | *******Only 8 experimental annotations to Frizzled-2 binding | ||
***** | *****Some annotation with terms like 'cytokine activity' | ||
******Should we have terms in the ontology like 'cytokine agonist activity' as a child of 'receptor agonist activity' | ******Should we have terms in the ontology like 'cytokine agonist activity' as a child of 'receptor agonist activity' and 'cytokine antagonist activity' as a child of 'receptor antagonist activity' | ||
*****General issue: co-annotation vs more terms in the ontology | |||
**MAPK - David H. and Sabrina | **MAPK - David H. and Sabrina | ||
***Examining gene products annotated to the process with no experimental support for known MFs | ***Examining gene products annotated to the process with no experimental support for known MFs |
Revision as of 17:21, 21 August 2017
Meeting URL
Agenda
Cambridge Meeting, October 2-4, 2017
- 2017 Cambridge GOC Meeting Logistics
- Registrration - confirm pay in cash
- 2017 Cambridge GOC Meeting Agenda
- Poster session Monday night
- Wednesday afternoon hands-on/workshop session. Suggestions:
- Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.
- Presentations from Val (PomBase), Mary Dolan (MGI)
- Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.
- Conventional annotation display as well as GO-CAM model display
- Good annotation practice: phenotype vs process
- Representing biologists’ view of biology
- Author intent & protein domains; IDA v IC v New evidence code
- Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.
2017 Cambridge GOC Signalling Workshop, October 1, 2017
- 2017 Cambridge GOC Signalling Workshop
- Start thinking about agenda
- We have four different pathways being worked on
- Four presentations, and time for a wrap-up?
- Summary of analysis work, followed by specific proposals?
- Some of the same annotations issues are surfacing for different pathways
- Four presentations, and time for a wrap-up?
Signaling Project
- Update on progress to date, github tickets
- Wnt - Giulia, Helen, Kimberly
- Google spreadsheet with annotation, ontology analysis
- Google doc for crystallizing github tickets
- Annotation and Ontology Issues:
- Wnts
- Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but generally an underused term
- Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common
- Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology
- Multiple frizzleds exist, but we only have a separate term for frizzled-2; 10 mammalian frizzleds, 2 (?) Drosophila frizzleds, 4 C. elegans frizzleds
- Only 8 experimental annotations to Frizzled-2 binding
- Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology
- Some annotation with terms like 'cytokine activity'
- Should we have terms in the ontology like 'cytokine agonist activity' as a child of 'receptor agonist activity' and 'cytokine antagonist activity' as a child of 'receptor antagonist activity'
- General issue: co-annotation vs more terms in the ontology
- Wnts
- 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
- Wnt - Giulia, Helen, Kimberly
Minutes
- On call: