Plant ontology updates

[Katica Ilic]

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


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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/
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Stanford, CA 94305
U.S.A.
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