Plant ontology updates

[Katica Ilic]

Pankaj,

I don't mind leaving vascular bundle out for now, but for the 'stem
vascular system' I see no major reason of not including it, I have a few
annotations sitting and waiting for this ter.
we already have the following terms in PO (in no particular order):

cotyledon vascular system
leaf vascular system
root vascular system
vascular system

and stem vascular system is clearly missing.

Whatever we decide on 'vascular bundle', the existance of this new term is
justified as a need for the grouping term which is required for annotation
(since we don't have term 'stele' in the PO, only 'root stele').

So, I would vote to introduce 'stem vascular system' in this round.

Let me know what you think.

Katica

On Wed, 4 May 2005, Pankaj Jaiswal wrote:

> I suggest leaving the vascular system and bundle terms until I come up
> with a proposal. Still working on those. Toby has some issues as well.
> Rest is fine, you can go ahead and add the terms I proposed to bring back.
>
> -Pankaj
>
> 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.
> > --------------------------------------------------------------------------
> >
> >
> >
>
> --
> ************************
> Pankaj Jaiswal, PhD
> G15-Bradfield Hall
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel: +1-607-255-3103
>       +1-607-255-4109
> Fax: +1-607-255-6683
> http://www.gramene.org
> ************************
>

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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.
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