Annotation Conf. Call 2017-05-09

Bluejeans URL

https://bluejeans.com/993661940

Agenda

Annotation Guidelines

Review Annotation Guidelines for Cellular Component (CC) Annotations

• Many gene products can be found in multiple places within the cells in which they are expressed
  • 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
  • Internalized receptors can be found in endocytic vesicles
  • Transcriptional regulators can shuttle between the cytoplasm and the nucleus
  • Secreted ligands can be found in the extracellular space and the external side of a plasma membrane when they are bound to their receptor
• The curation guidelines for CC annotation are to annotate the gene product to the cellular/extracellular location where it is believed to be active
  • For some gene products this will be very clear
  • There are some cases where receptors found at the plasma membrane are also found to be involved in signaling pathways that occur at other locations
    • PACAP1 receptor - endocytic vesicle
    • Trk - Golgi
  • What if you don't know whether a subcellular location is a site of molecular activity?

Use of colocalizes_with Qualifier

• 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.

Annotation and Ontology Proposals

Modification-Dependent Protein Binding

• Proposal from Pascale and Sylvain emailed
• Would like to review and approve proposal on this call

Transcription Decision Tree

• AI: Review annotation decision tree which is linked from the github ticket in go-annotation
• github ticket 1463