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Planteome / plant-trait-ontology

Explore the Plant Trait Ontology on the Planteome site.
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height trait (TO:0000171) - and child terms #226

Open planteome-user opened 11 years ago

planteome-user commented 11 years ago

Currently this has one child:

..is_a stature or vigor trait (TO:0000133) : A subjective assessment of the plant in similar site and growing conditions (often unfavorable conditions) based upon a specific facet of growth.

..is_a (TO_0000171) height related trait : "Height related traits." ....is_a TO:0000207 plant height DEF: " A stature and vigor trait (TO_0000133) which is associated with the height of a whole plant (PO:0000003).

Reasoner report yields:

NEW, INFERRED [SubClassOf (TO:0000541](http://purl.obolibrary.org/obo/SubClassOf %28TO_0000541%29 'leaf height' [TO:0000171]%28http://purl.obolibrary.org/obo/TO_0000171) 'height related trait') NEW, INFERRED SubClassOf(TO:0000682 'inflorescence height' TO:0000171 'height related trait')

Reported by: cmungall

Original Ticket: obo/plant-trait-ontology-to-requests/225

planteome-user commented 10 years ago

proposed new children of height related trait

Change relation of inflorescence height from inflorescence anatomy and morphology trait to height related trait

inflorescence height (TO:0000682): A height related trait (TO:0000171) which is associated with the height of an inflorescence (PO:0009049) measured from ground to the attachment point.

change name and relation of ear height to ear infructescence height and a child of height related trait

ear infructescence height (TO:0000683): A height related trait (TO:0000171) which is associated with the height of an ear infructescence (PO:0025597) measured from the ground to the attachment point.

Original comment by: lauramooray66

cooperl09 commented 9 years ago

In common language usage "height" really has two meanings; how tall something or someone is and also how "high up" something is.

For example in the TO, we have plant height (TO:0001003) ie: how tall the plant is, and also terms like leaf height (TO:0000541)- how high up on the stem the leaf is.

On carefully review of the PATO definition, It is clear that this encompasses only the former meaning of "height" (ie: tallness): height (PATO:0000119): A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.

height (PATO:0000119): is child of "size", thus it does not describe how high up something is.

I propose using separates term to describe the position of a plant structure, ie: how high up it is from the ground or other point of reference. Xref: position (PATO: 0000140): A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.

cooperl09 commented 9 years ago

Revised name and definition: Was: height related trait (TO:0000171): A stature and vigor trait (TO:0000133) which is height.

Revised: A stature and vigor trait (TO:0000133) which is the height of a whole plant (PO:0000003) or another plant structure (PO:0009011).

Comment: Refers to: height (PATO_0000119): A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.

cmungall commented 9 years ago

very good point!

But I think you need new subclasses of distance to be able to make definitions. E.g.

Even 'normal' height is hard for plants. Is this distance of top of organism from substrate? Start of roots? Does the plant height decrease if I pile some dirt around the base?

cooperl09 commented 9 years ago

re: "Even 'normal' height is hard for plants. Is this distance of top of organism from substrate? Start of roots? Does the plant height decrease if I pile some dirt around the base?"

Agreed, but these are all methods that can be specified for the exact situation. In the reference term, we would not specify the means of measuring it.

cooperl09 commented 9 years ago

Please see #84 for plant height (TO:0000207).

cooperl09 commented 9 years ago

ear infructescence height (TO:0000683): A height related trait (TO:0000171) which is the height of an ear infructescence (PO:0025597) measured from the ground to the attachment point.

Revised name and definition: ear infructescence position (TO:0000683): An ear infructescence morphology trait (TO:0000976) which is the position of an ear infructescence (PO:0025597).

Comment: Refers to: position (PATO_0000140): A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. In maize this is usually measured from the ground to the attachment point of the ear.

**Revised name and definition: ear position (TO:0000966): An ear infructescence morphology trait (TO:0000976) which is the ratio of ear height to plant height.

ear infructescence position ratio (TO:0000966): An ear infructescence morphology trait (TO:0000976) which is the ratio of ear infructescence position (TO:0000683) to plant height (TO:0000207). See also #132

cooperl09 commented 8 years ago

Deprecating this grouping term as the child terms have been moved: height trait (TO:0000171): A stature and vigor trait (TO:0000133) which is the height of a whole plant (PO:0000003) or another plant structure (PO:0009011).