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#281 stages: isa or partof?

Anatomy or Morphology Trait
closed-rejected
nobody
None
5
2014-07-05
2014-07-05
Chris Mungall
No

PO:0007615 ! flower development stage *** [DEF: "A reproductive shoot system development stage (PO:0025530) which begins with the onset of the flower meristem transition stage (PO:0025588) and ends after the flowering stage (PO:0007616)."]

This is a perfect definition. Here it is drawn out (with time running left to right)

    |--------- flower development stage -----------|
    |--FMTS------| ?????????????????  |----FS--| ???

From the definition and the diagram it's clear that FMST and FS are parts of FDS.

However, in PO, FMTS and FS are declared subclasses of FDS.

What does this mean? For one thing, the properties of the parent are inherited over subclass. This means that FS inherits the property of ending after FS (as this is declared in the definition of FDS). This is obviously not what was intended.

It follows from this that subclass doesn't make sense here. Either

  1. Change the relation to part_of OR
  2. Change the definition to "A reproductive shoot system development stage (PO:0025530) which is one of the stages that begins with the onset of the flower meristem transition stage (PO:0025588) and ends after the flowering stage (PO:0007616)."

Related

Plant Trait Ontology (TO) requests: #281

Discussion

  • Laurel Cooper

    Laurel Cooper - 2014-07-05

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    Hi Chris,

    I appreciate you posting these comments on the tracker, but suggest
    this should really go on the relevant Plant Ontology tracker for
    flower development  stages:



    http://sourceforge.net/p/obo/plant-ontology-po-term-requests/500/



    Thanks

    Lol



    On 7/5/14 12:30 PM, Chris Mungall
    wrote:





    [plant-trait-ontology-to-requests:#281]
    stages: isa or partof?


    Status: open

    Branch: Anatomy or Morphology Trait

    Created: Sat Jul 05, 2014 07:30 PM UTC by
    Chris Mungall

    Last Updated: Sat Jul 05, 2014 07:30 PM UTC

    Owner: nobody


    PO:0007615 ! flower development stage *** [DEF: "A
    reproductive shoot system development stage (PO:0025530)
    which begins with the onset of the flower meristem
    transition stage (PO:0025588) and ends after the flowering
    stage (PO:0007616)."]


    This is a perfect definition. Here it is drawn out (with time
    running left to right)



        |--------- flower development stage -----------|
    
    |--FMTS------| ?????????????????  |----FS--| ???


    From the definition and the diagram it's clear that FMST and
    FS are parts of FDS.


    However, in PO, FMTS and FS are declared subclasses
    of FDS.


    What does this mean? For one thing, the properties of the
    parent are inherited over subclass. This means that FS
    inherits the property of ending after FS (as this is declared
    in the definition of FDS). This is obviously not what was
    intended.


    It follows from this that subclass doesn't make sense here.
    Either



    1. Change the relation to part_of OR

    2. Change the definition to "A reproductive shoot system
      development stage (PO:0025530) which is one of the
      stages that       begins with the onset of the flower
      meristem transition stage (PO:0025588) and ends after the
      flowering stage (PO:0007616)."



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    -- 
    

    

    Laurel (Lol) Cooper, PhD
    
Coordinator, Plant Ontology Consortium
    
Dept. of Botany and Plant Pathology
    
Rm 3086, Cordley Hall
    
Oregon State University
    
Corvallis, OR 97331
    
Web: www.plantontology.org
    

    Phone: 541-737-5272
    
Fax: 541-737-3573
    
Skype: cooperlol910
    
***********

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    Related

    Plant Trait Ontology (TO) requests: #281

  • Chris Mungall

    Chris Mungall - 2014-07-05
    • status: open --> closed-rejected
     

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