Annotation Conf. Call 2017-05-09: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 67: Line 67:


= Minutes =
= Minutes =
*On call:
*On call: Alice, David H., Edith, Emily, Harold, Helen, George, Midori, Moni, Rachael, Sabrina, Shur-Jen, Stan, Val





Revision as of 11:01, 9 May 2017

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)

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
  • 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

 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
    • 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, Midori, Moni, Rachael, Sabrina, Shur-Jen, Stan, Val