Annotation relations and qualifiers

[dosumis]

GPAD specifies the relationships between the subject of annotation (GP, complex) and a primary GO term. T Relations are:

• part_of: CC
• enables: MF
• involved_in: BP

his relationship may be modified by the use of qualifiers:

• colocalizes_with: CC
• contributes_to: MF

The relevant relations are in RO, but should be made more visible to tools used by curators. Usage statement on these relations should live in gorel and reflect agreed semantics (Right now doc of qualifiers lives in the GOA DB*)

Plan: Pull these relations into gorel and add usage statements, reconciling guidance developed by curators with agreed semantics.

*From QuickGO:

• 'Contributes_to'
  • User guide: appears in a GO annotation when a function of a protein complex is facilitated, but not directly carried out by one of its subunits. GO Consortium documentation
  • Curation guide: An individual protein that is part of a complex can be annotated to terms that describe the action of the complex. This qualifier allows us to distinguish individual subunit from complex functions e.g. This protein contributes_to 'ribosome binding' when part of a complex but does not perform this function on its own.
• 'Colocalizes_with'
  • User guide: appears in a GO annotation to indicate a transient or peripheral association of the protein with an organelle or complex. GO Consortium documentation
  • Curation guide: Proteins 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.

CC @mcourtot @tonysawford

[dosumis]

Progress:

Made all of these children of 'go_annotation_extension_relation' object property. This is clearly overloading, but is currently the only method usable pulling across object properties to gorel.(owl||obo) (and let's face it - this is a hack in the first place).

TODO - work on usage statements.