Plant ontology updates

[Katica Ilic]

Toby,

This certainly clarifies it for me. We need to think of the best way to
include this in the definition/comment section.

Katica

On Wed, 4 May 2005, kellogge wrote:

> 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/
> home.html
>

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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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