Changes between Version 51 and Version 52 of RelationsAndTransitivity


Ignore:
Timestamp:
Mar 9, 2015, 3:15:06 PM (6 years ago)
Author:
vw253
Comment:

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  • RelationsAndTransitivity

    v51 v52  
    22
    33= Describing How Annotation is Propagated over relations in FYPO =
     4
     5Note: It isn't really correct to refer to ancestors and descendants for some of these relations
    46
    57= output of =
     
    2426  * '''A.''' FYPO:0002797 decreased protein degradation '''has_output B''' FYPO:0000836 increased protein level
    2527 
    26 
    2728Annotations should propagate over '''has_output''' ('''A has_output B''' : all of B should annotated to A)
    2829  * i.e. In the PomBase Query builder all '''FYPO:00''' should be annotated to '''FYPO:000'''
     
    4041
    4142= has_part =
     43
     44'''Examples:'''
     45  * '''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?)
     46 
     47Annotations should propagate over '''has_part''' from the "whole" to the "part" ('''A has_part B''' : all of A should annotated to B)
     48  * i.e. In the PomBase Query builder all '''FYPO:0001490''' should be annotated to '''FYPO:0000049'''
     49
     50In Canto we should see the '''has_part''' related terms as ancestors
     51  * i.e.    '''FYPO:0000049 inviable cell ''' should be visible as a ancestor of ''' FYPO:0001490  inviable elongated vegetative cell'''
     52
     53[[br]]
     54[[br]]
     55
    4256show term2 on the list of "child" terms if the ontology has a "term2 has_part term1" link
    43 Propagation should be from the "whole" to the "part"
    4457if B has_part A, all genes annotated to B should annotated to A (and not necessarily vice versa)
    4558This should ONLY be done for FYPO; GO annotations should (continue to) not be propagated over has_part in either direction
    4659
    47 notes:
    48 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