Feedback Submission from Plant Ontology Live Site

[Pankaj Jaiswal]

Dear Dr. Alison,

Thank you for your suggestion. We really appreciate your feedback and 
hope to provide the best possible vocabulary of plant anatomy.

Please look for my comments next to your suggestions.

Best regards
Pankaj

feedback_submission at brie4.plantontology.org wrote:

>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: I teach a plant anatomy course at the University of Rhode Island and I have struggled with presenting antomical terms heirarachically for many years. I believe PO will be an excellent resource and I plan on having my students use it extensively. 
> 
> Over the last few week I have been working to make the terminology I use in class consistent with PO and have encountered a few difficulties.
> 
> 1.  The term "pericycle" (PO:0006203) is defined as "part of the tissue of the stele", yet it is listed as a child of the stem cortex. But, the cortex EXCLUDES the stele, being defined as occuring BETWEEN the vascular system (i.e. the stele) and epidermis.
> 
I agree with you and propose to organize this as follows by
-deleting the relationship pericycle is part_of root cortex relationship
-creating a new relationship pericycle is part_of root stele

---PO:0009075 : plant ontology
----i PO:0009011 : plant structure
-------i PO:0009003 : sporophyte
-----------p PO:0009005 : root
--------------p PO:0000258 : root cortex
--------------p PO:0020124 : root stele
-------------------p PO:0006203 : pericycle
-------i PO:0009007 : tissue
-----------i PO:0005708 : cortex
--------------i PO:0000258 : root cortex
--------------i PO:0006203 : pericycle



> 2.  The "cortex" (PO:0005708) includes the tissues "endodermis" and "hypodermis", but not "parenchyma", "collenchyma", "sclerenchyma", which are listed as separate tissue. This is related to the next point.
> 

It is so because the terms like parenchyma, collenchyma and sclerenchyma 
are generic tissue terms and there are many such instances, of these 
tissue types that are not always present in cortex. Whereas endodermis 
and hypodermis if found are always part of cortex.

I just looked at the tree and propose for making following generic terms 
as part_of generic term for PO:0005708 : cortex.

  PO:0000252 : endodermis
  PO:0005051 : hypodermis



> 3.  In most texts, the cortex (and also the pith) are not considered "TISSUES", but are described as "regions". Although the terms "cortex" and "pith" are useful and widely used, they do not fit well into a classification. Perhaps these terms should become obsolete as has "ground tissue". If "cortical parenchyma" and "pith parenchyma" are added as types of parenchyma, then all tissues of pith and cortex (both stem and root) will be accounted for.
> 
We are looking into your suggestions and will get back to you soon.


> Thank you for your efforts,
> Alison Roberts
> 
> name: Alison Roberts
> 
> email: aroberts at uri.edu
> 
> organization: University of Rhode Island
> 
> send_feedback: Send your feedback
> 
> 

-- 
************************
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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