wiki:RelationsAndTransitivity

Version 35 (modified by vw253, 6 years ago) (diff)

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Describing How Annotation is Propagated over relations in FYPO

output of

Annotations should propagate over output_of B output_of A all of B should be annotated to A

show term2 on the list of "child" terms if the ontology has a "term2 has_part term1" link

has_output

Examples:

  • A. FYPO:0001270 complete but unequal mitotic sister chromatid separation has output 'B FYPO:0000284 large and small daughter nuclei
  • A. FYPO:0002797 decreased protein degradation

has_output has output B FYPO:0000836 increased protein level

Annotations should propagate over has_output (A has_output B : all of B should annotated to A)

  • i.e. In the PomBase? Query builder all FYPO:0000284 large and small daughter nuclei should be annotated to FYPO:0001270 complete but unequal mitotic sister chromatid separation

In Canto we should see the has_output related terms as descendants

  • i.e. FYPO:0000284 large and small daughter nuclei should be visible as a descendent of FYPO:0001270 complete but unequal mitotic sister chromatid separation



results_in_formation_of

Annotations should propagate over results_in_formation_of results_in_formation_of A all of B should annotated to A

has_part

Propagation should be from the "whole" to the "part" if B has_part A, all genes annotated to B should annotated to A (and not necessarily vice versa) This should ONLY be done for FYPO; GO annotations should (continue to) not be propagated over has_part in either direction

notes: I put child in scare quotes because if we do this, the parent/child nomenclature becomes less accurate and less meaningful. I'm not sure whether we should fret about it in the context of the curation tool, but it's generally true for a lot of the different sorts of newfangled relations that are coming on line in GO, FYPO, and others