Question about PO term 'Whole plant' (fwd) (PR#57)

[Katica Ilic]

Hi David,

The term 'whole plant' was introduced to the PO for the purpose of facilitating
annotations (when no other term could be used). It was introduced as a
necessity, it is not really a botanical term, has vague meaning (and
definition), and other terms that are available in the Plant Ontology should be
used instead (such as sporophyte).

Since we don't encourage users to use this term extensively, but rather
scarcely, that is, only when absolutely necessary, we deliberately chose no to
have any terms as children of 'whole plant'. Moreover, we have considered moving
this term in a separate 'placeholder bin' in the ontology, so that it wouldn't
appear as a top node.

When creating this ontology, we decided that 'true'' top nodes (as an
instance_of) of the Plant Structure are: 
cell
tissue
gametophyte
sporophyte

(we eliminated 'organ' to avoid redundancy in the ontology). Additional two
nodes, 'in vitro cell, tissue and organ culture' and 'whole plant' are really
'satellite' nodes and are included to provide terms required for gene
annotations. 

Terms that you listed are already in the ontology, they are children of the top
node 'sporophyte', where they belong, as they are parts of the sporophyte.

The 'above and below ground plant parts' division that you mentioned is not
really relevant for the Plant Structure Ontology. 

I hope this clarifies the organization of the top nodes in the Plant Structure
Ontology. If you would like to learn more about organizing principles of PO,
please visit the following
URL:http://www.plantontology.org/docs/otherdocs/principles_rationales.html.


Best regards,

Katica Ilic, POC Project Coordinator


> ---------- Forwarded message ----------
> Date: Fri, 29 Apr 2005 06:27:46 -0400
> From: owner-po-dev at brie4.cshl.org
> To: katica at acoma.Stanford.EDU
> Subject: BOUNCE po-dev at brie4.cshl.org:[David Craigon
<david at arabidopsis.info>]
> 
> Hello,
> 	I'd like to ask a naive question about the plant ontology. I was
> wondering why all terms were not "part-of" the "whole plant"? I'd like a
> section of the tree that goes something like:
> 
> Whole plant-----above ground parts----leaves
>             |    |
>             |    |---------------------flowers (and so on)
>             |
>             |----below ground parts----roots
> 
> That way as you move down the tree the areas of the plant gets more
> specific a la GO, and as you get to the bottom you get all the way down
> to cells.
> 
> You could still have a cells, tissues, etc. category at the top as well,
> since each child term could be in both categories.
> 
> What do you think? Is this too simplistic?
> 
> 
> 		David
> 
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: katica at acoma.stanford.edu	
The Arabidopsis Information Resource	Tel: (650) 325-1521 ext. 253	
Carnegie Institution of Washington	Fax: (650) 325-6857	
Department of Plant Biology	        URL: http://arabidopsis.org/		
260 Panama St.
Stanford, CA 94305, U.S.A.