Annotation Conf. Call 2017-05-09
Bluejeans URL
https://bluejeans.com/993661940
Agenda
GOC Meeting, Corvallis, OR, June 1-3rd
- Meeting Agenda
- Review items; link to github tickets (create a ticket if none exists)
- Poster session
Annotation and Ontology Proposals
Modification-Dependent Protein Binding
- Proposal from Pascale and Sylvain emailed
- Would like to review and approve proposal on this call
The proposal is the comment near the end of issue: https://github.com/geneontology/go-ontology/issues/12787
(text starts with "Here's a version of the proposal, reviewed by the GO-editors and by @sylvainpoux"
Transcription Decision Tree
- AI: Review annotation decision tree which is linked from the github ticket in go-annotation
- Reminder to review the current state of the proposal on the github tracker
- github ticket 1463
Annotation Guidelines
Review Annotation Guidelines for Cellular Component (CC) Annotations
- GO Cellular Component annotations are meant to capture the location where a gene/gene product is active, i.e. where it executes its molecular function
- Gene products can be found in multiple places within the cells in which they are expressed
- Some of those locations reflect where it is believed to act, others not
- Gene products that are transported by the secretory pathway
- Soluble secreted proteins and transmembrane proteins can be found in a number of different cytoplasmic compartments (ER, Golgi, vesicles) as they traverse the secretory pathway
- Gene products that are relocalized as part of the regulation of their activity
- Internalized receptors and/or ligands can be found in endocytic vesicles
- Transcriptional regulators can shuttle between the cytoplasm and the nucleus
- Gene products that are transported by the secretory pathway
- Some of those locations reflect where it is believed to act, others not
- Curators should use existing knowledge about the functions and processes of the gene/gene product to determine what is an appropriate annotation
- For example, we don't want to say, categorically, that a receptor could never be annotated to an endocytic vesicle or a component of the secretory pathway, but if the annotation is made, it's because there is positive evidence that the receptor has a function there
- Annotation questions
- Is it appropriate to annotate a membrane-bound ligand expressed in a signaling cell to a location in a receiving cell?
- ZP3 (zona pellucida glycoprotein) found in oocytes to 'outer acrosomal membrane' (of sperm cell)
- Notch - Delta signaling is another example
- What if you don't know whether a subcellular location is a site of molecular activity?
- A novel protein expressed in multiple locations; mutations in the encoding gene affect known processes
- Is it appropriate to annotate a membrane-bound ligand expressed in a signaling cell to a location in a receiving cell?
Use of colocalizes_with Qualifier
- Early on in GO there was discussion about how to annotate genes/gene products that are sometimes found in association with a given CC
- Current documentation:
Gene products that are transiently or peripherally associated with an organelle or complex may be annotated to the relevant cellular component term, using the colocalizes_with qualifier. This qualifier may also be used in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member. Example (from Schizosaccharomyces pombe): Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p is annotated to spindle pole body; GO:0005816 and contractile ring; GO:0005826, using the colocalizes_with qualifier in both cases.
- Discussion Points
- Assay resolution
- A qualifier used when the level of resolution of an assay did not allow for unambiguous determination of localization
- Peripheral association
- Transient association
- Gene/gene products can be found in multiple locations for a defined period of time, but if that location is where they function, curators do not need to use the colocalizes_with qualifier
- If possible, curators can use annotation extensions to provide more information about the phase or stage during which the localization is observed
- Example of a transcription factor that is present in the cytoplasm but then moves to the nucleus to function in response to a stimulus
- If possible, curators can use annotation extensions to provide more information about the phase or stage during which the localization is observed
- If the gene/gene product is not believed to function in a particular location, use of colocalizes_with is not warranted
- Gene/gene products can be found in multiple locations for a defined period of time, but if that location is where they function, curators do not need to use the colocalizes_with qualifier
- Use of colocalizes_with and complex annotations
- should we really use "colocalizes_with" with cc complex terms
- Are some of the CC annotations using colocalizes_with referring instead to complex binding?
- Are immunofluorescence experiments sufficient to demonstrate colocalizes_with a complex?
- IPR028867/IPR028868 mappings to glutamate receptor complex (GO:0032983)
- Question about auxiliary subunits of receptor complexes
- should we really use "colocalizes_with" with cc complex terms
- Can we deprecate colocalizes_with? Do we now have better ways to describe what we were trying to capture with this qualifier?
- Assay resolution
Minutes
- On call: Alice, David H., Edith, Emily, Harold, Helen, George, Giulia, Karen, Kevin, Midori, Moni, Petra, Rachael, Sabrina, Seth, Shur-Jen, Stacia, Stan, Tanya, Val
GOC Meeting, Corvallis, OR, June 1-3rd
- Please check the agenda, add items, if needed
- Link all items to a github ticket
Annotation and Ontology Proposals
Modification-Dependent Protein Binding
- New proposal from Pascale and Sylvain
- Want to capture binding events that are *dependent* on a particular PTM, not just binding of a gene product that has a PTM
- Annotations to existing terms will need to be reviewed; will try not to obsolete terms and create new ones, but curators will likely need to review annotations