wiki:RelationsAndTransitivity

Version 52 (modified by vw253, 6 years ago) (diff)

--

Describing How Annotation is Propagated over relations in FYPO

Note: It isn't really correct to refer to ancestors and descendants for some of these relations

output of

Examples:

  • A. FYPO:0000284 large and small daughter nuclei output_of B FYPO:0001270 complete but unequal mitotic sister chromatid segregation

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

  • 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 segregation

In Canto we should see the output_of 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 segregation



has_output

Examples:

  • A. FYPO:0002797 decreased protein degradation 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:00 should be annotated to FYPO:000

In Canto we should see the has_output related terms as ancestors

  • i.e. FYPO:0000836 increased protein level should be visible as a ancestor of FYPO:0002797 decreased protein degradation



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

Examples:

  • A. FYPO:0001490 inviable elongated vegetative cell has_part B FYPO:0000049 inviable cell (NOTE I AM NOT SURE IF THIS IS A GOOD EG AS I THINK THERE ARE ALO IS_A LIKS HERE?)

Annotations should propagate over has_part from the "whole" to the "part" (A has_part B : all of A should annotated to B)

  • i.e. In the PomBase? Query builder all FYPO:0001490 should be annotated to FYPO:0000049

In Canto we should see the has_part related terms as ancestors

  • i.e. FYPO:0000049 inviable cell should be visible as a ancestor of FYPO:0001490 inviable elongated vegetative cell



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