planteome-user
commented
10 years ago 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
[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: nobodyPO: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
- Change the relation to part_of OR
- 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 ***********************************************************
Original comment by: cooperl09
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)
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
Reported by: cmungall
Original Ticket: obo/plant-trait-ontology-to-requests/281