Annotation Conf. Call 2017-08-22
Meeting URL
Agenda
Cambridge Meeting, October 2-4, 2017
- 2017 Cambridge GOC Meeting Logistics
- Registration - 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
- Possible proposal: Add terms like 'Wnt receptor agonist activity' and 'Wnt receptor antagonist activity'
- Note that we have terms like 'Wnt-activated receptor activity' to describe receptors
- Is this a generally reasonable and sustainable approach for describing the activity of signaling ligands and their receptors?
- 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; this would be in agreement with synonyms for 'Wnt-activated receptor activity'
- Multiple frizzleds exist, but we only have a separate term for frizzled-2; 11 mouse and human frizzleds, 4 Drosophila frizzleds, 4 C. elegans frizzleds
- Only 8 experimental annotations to Frizzled-2 binding
- Related proposal: Move 'smoothened binding' to be a sibling, rather than child, of 'frizzled binding' . See: Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse and Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface
- Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology; this would be in agreement with synonyms for 'Wnt-activated receptor activity'
- Some annotation with terms like 'cytokine activity'
- Should we have terms in the ontology like 'cytokine receptor agonist activity' as a child of 'receptor agonist activity' and 'cytokine receptor antagonist activity' as a child of 'receptor antagonist activity'
- The 'cytokine' term definition in GO is very broad ("Functions to control the survival, growth, differentiation and effector function of tissues and cells.”), so annotations to Wnts fit the definition. But, do researchers really think of Wnts as cytokines?
- General issue: co-annotation vs more terms in the ontology
- Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but generally an underused term
- Receptors
- Frizzleds are 7-transmembrane proteins that are class F members of the GPCR family of receptors
- Most frizzleds, however, do not appear to signal via G-proteins
- Proposal: Create a specific term for Wnt-activated GPCR activity
- 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: