Plant ontology updates

[Pankaj Jaiswal]

Fine.
-Pankaj

Katica Ilic wrote:

> 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
>>************************
>>
> 
> 
> --------------------------------------------------------------------------
> 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
************************