#597 stages: isa or partof?

[Chris Mungall]

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)."

[Ramona Walls]

Many of the stages in the PO are defined so that shorter segments of a potentially longer stage are subclasses of the longer stage. This is done by using wording like "occurs during the interval between...". See for example sporophyte vegetative stage or secondary xylem development stage.

I am in favor or redefining the flower development stages so that they are similar to the other development stages.

[Barry Smith]

I believe the answer is as follows:

I believe that the solution is as follows (and that this solution is already applied in parts of the PO):

all X stages are is_a children of the class / type X stage

for each value of 'X' we have a maximal stage, and all X stages including this maximal stage, are part-of this maximal stage

the maximal stage might be called 'life of X'
or 'life cycle of X'
or 'whole life of X'

or some such
BS

[Ramona Walls]

What Barry has proposed is similar to what we have done for whole plant development stage, which has "life of whole plant" as a subclass, where life of whole plant is define as a maximal whole plant development stage (bearing in mind Chris's concern about the working of that definition, as he expressed in the manuscript). Because "gametophyte development stage" and "sporophyte development stage" are part_of "life of whole plant", every other whole plant development stage which is a subclass of one of those classes is therefore also part_of "life of whole plant'.

Adding a similar maximal stage for all the other structures would be quite time consuming, so if this is adopting, it will probably have to wait for renewed funding.

For "flower development stage" and subclasses, I think we can proceed in the short term by rewording the definitions to better match the ontology structure.

[Ramona Walls]

I am working on specific suggestions for new definitions, which I will post under issue #500.