Plant ontology updates

[Pankaj Jaiswal]

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
************************