Plant ontology updates

[kellogge]

The difficulty with the root terms is created by the differences in  
root anatomy.  In monocots plus a few of the early-diverging  
angiosperms (e.g. Piperaceae), the vascular system of the root is made  
up of vascular bundles scattered all over the place as seen in cross  
section, and not organized into a central cylinder.  In eudicots, the  
term root vascular bundle doesn't have much meaning, since the stele is  
a cylindrical unit without separate bundles.  Thus for monocots and  
Piperaceae, you'd need the terms root vascular bundle and root vascular  
system (all the bundles as a group), whereas in eudicots and other of  
the early diverging lineages you'd need stele (which would include the  
endodermis) and root vascular system, which would be the vascular  
tissue encompassed by the stele.  So the accurate definition of the  
terms - to avoid confusing the annotators - would have to include some  
sort of comment on where the terms are to be applied.
Toby

On May 3, 2005, at 7:09 PM, Katica Ilic wrote:

> Hi all,
>
> The following changes to the Plant Structure Ontology are to be made  
> this
> week:
>
> I. Bringing back from the obsolete node terms 'crown root' and 'seminal
> root', and obsoleting 'nodal root'
>
> Ontology structure:
>
> adventitious root
>   % crown root ; PO:0003008
>   % seminal root ; PO:0003009
>
> Please, let me know if term 'brace root' is needed at present time.
>
> II. From St Louis meeting, the following terms are to be added (which  
> we
> already agreed on):
>
> New term:
> 1. stem vascular system
> Def: Total of the vascular tissues in their specific arrangements in  
> the
> stem.
>
> 2. root vascular bundle (new term, requested by Pankaj)
> Def: A strandlike part of vascular system of root, composed of phloem,
> xylem and associated transfusion tissue
>
> 3. add 'leaf vascular bundle' as a synonym of 'leaf vein'
>
> NOTE: we now have three highly redundant terms: root vascular system,  
> root
> stele and root vascular bundle. For a curator, it is going to be a very
> arbitrary decision to make on which one to use for annotation.
>
> 4. Renaming the term 'nodule' to 'root nodule' and adding a new  
> structure
> for the term 'nodule:
>
> New term: adventitious root nodule (syn. stem nodule)
> Def:  Enlargement or swelling on adventitious aerial roots in some  
> legumes
> (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria.  
> Unlike
> the root nodules, these contain functioning chloroplasts in the nodule
> cortex and are therefore capable of carbon fixation. (TAIR:ki)
>
> Ontology structure:
>
> root
>  (p) root nodule
>  (i) adventitious root
>      (p) adventitious root nodule (synonym: stem nodule)
>
>
> IV. Corrections of typos and minor errors in the ontology file :
> 1. Term: stem cortex
> Definition: The primary tissue located between the vascular system and  
> the
> epidermis of the root.
> (It should be 'of the stem").
>
> 2.	Sillica cell to silica cell
>
> 3. Cotyledon vascular system (to correct the definition)
>
> 4. Also, several minor typos in the text of the following:
> Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium.
>
> Thanks,
>
> Katica
>
>
> ----------------------------------------------------------------------- 
> ---
> Katica Ilic             		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.
> ----------------------------------------------------------------------- 
> ---
>
>
>
Elizabeth A. Kellogg
E. Desmond Lee and Family Professor of Botanical Studies
Department of Biology
University of Missouri-St. Louis
St. Louis, MO 63121
Tel: 314-516-6217
FAX: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ 
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