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
• 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
    • GPCR signaling from endosomes
• 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

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
  • component annotations and transient association
• 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 the gene/gene product is not believed to function in a particular location, use of colocalizes_with is not warranted
  • 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
  • Can we deprecate colocalizes_with? Do we now have better ways to describe what we were trying to capture with this qualifier?

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 (and their children) will need to be reviewed; will try not to obsolete terms and create new ones, but curators will likely need to review annotations to make sure they are consistent with the proposal