Feedback on POC: granular terms under 'petiole' (PR#56)

[Ruth De Groodt]

Dear Katica,


   I am indeed involved in a functional genomics project. For analysis
   of whole mounts and description of patterns we wanted to use a
   standardized nomenclature and looking for a solution, we found the
   website. As  I saw that in leaf lamina and roots, terminology goes
   quite in detail, since different cell/ tissue layers are defined,
   and as I wanted to describe my results as far as I can see the
   pattern of expression with a normal DIC microscope, I saw that with
   petioles there were lacking a few terms describing layers that can
   be distinguished fairly easy like epidermis, cortex and vascular tissue.
   I agree that for the vascular tissue in petioles, it's difficult to
   distinguish different layers in whole mounts (on sections you can!),
   but to be complete I add them in my suggestion.

   I hope this is an answer to your question.

   kind regards,


   Ruth

Katica Ilic wrote:

>Dear Ruth,
>
>Thanks for the feedback and suggestion for improving current Plant Ontology
>structure. Term 'petiole' does not have any granular 'children' terms yet, since
>we deliberately chose not to have very detailed and elaborate ontology, at least
>not in the initial stage when we were focused on creating a robust and
>extensible structure as a backbone to which granular terms can be added as
>needed. 
>
>Our group is now considering your suggestion for adding more granular terms for
>'petiole', and I have a couple of questions, to make sure that we can
>accommodate what you would like to see in this segment of the ontology, at the
>same time, making sure that we keep the Plant Ontology 'generic', encompassing
>both, dicots and monocots. I am assuming that these terms are required for
>functional genomics project that you might be involved and I wonder if a simpler
>solution that does not have, for instance 'interfascicular parenchyma' would
>work. I'll get back to you soon with the outline of the structure we are
>currently considering, but in the meantime, it would be useful if you can tell
>us few fords about the specific reasons for inquiring the structure you proposed
>and also how you use the Plant Ontology.
>
>Thank you again for sending us your suggestion. I look forward to hearing from
>you.
>
>Best regards,
>
>Katica Ilic, POC Project Coordinator
>
>
>  
>
>>---------- Forwarded message ----------
>>Date: Wed, 20 Apr 2005 04:02:29 -0400
>>From: feedback_submission at filetta.cshl.edu
>>Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu
>>To: po-dev <po-dev at plantontology.org>
>>Subject: Feedback on POC
>>
>>    *** Feedback from Plant Ontology Live Site ***
>>
>>refer_to_url: http://www.plantontology.org/index.html
>>
>>comments: To whom it may concern:
>>
>>This message proposes a refinement of the anatomical ontology.
>>
>>In dicotelydons, the petiole, like the stem, consists of a dermal, fundamen=
>>tal (ground) and vascular system.  Its epidermis consists in one layer of c=
>>ells and contains elongated epidermal cells and stomatal complexes, althoug=
>>h the latter occur less frequently in petioles than in leaf lamina. Under t=
>>he epidermal layer is the ground tissue of which the outer region is the co=
>>rtex and the inner region is the pith. These two regions are interconnected=
>> by the interfascicular parenchyma. In the vascular system (stele), the vas=
>>cular bundles (xylem and phloem) are separated by this interfascicular pare=
>>nchyma. The pith is located in the very centre of the stele.
>>
>>This organisation can be summarized as follows, from the outside in:
>>
>>Petiole
>>=B7=09dermal system
>>              - epidermis
>>              - stomatal complex
>>=B7=09cortex
>>=B7=09vascular system
>>              - phloem
>>              - xylem
>>              - interfascicular parenchyma
>>              - pith
>>
>>As there is presently no subdivision under the term =93petiole=94, would it=
>> be possible to add these categories in the ontology tree?  Definitions of =
>>the terminology used above are similar to those listed in the current ontol=
>>ogy  but are here applied for petioles. Do not hesitate to contact us back =
>>if you need any additional information regarding this proposal.
>>
>>
>>Ruth De Groodt
>>Bj=F6rn De Meyer
>>Pierre Hilson
>>
>>
>>name: Ruth De Groodt
>>
>>email: ruth.degroodt at psb.ugent.be
>>
>>organization: VIB - Department of Plant Systems Biology
>>
>>send_feedback: Send your feedback
>>
>>
>>
>>    
>>


-- 
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Ruth De Groodt                                 TEL:32 (0)9 3313846
PLANT SYSTEMS BIOLOGY                          Fax:32 (0)9 2645349
Department of Functional Genomics
GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium
Vlaams Instituut voor Biotechnologie                           VIB
mailto:rugro at psb.UGent.be    	   http://www.psb.UGent.be
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