Feedback on POC: granular terms under 'petiole' (PR#56)
Ruth De Groodt
rugro at psb.ugent.be
Fri Jun 10 09:36:58 EDT 2005
Hi Katica,
for the leaves it's fine for me now. Maybe in the future I will submit
some proposals for roots, but I still have didn't have a close look at
that part. I the future, I will have to do a detailed analysis on that
as well.
I will let you know.
best regards,
Ruth
Katica Ilic wrote:
>Hi Ruth,
>
>I am glad to hear that proposed structure worked for you. Please let us know if
>you would like to see additional, more granular terms in PO.
>
>Thank you for using Plant Ontologies and for contacting us. Your suggestions and
>comments are greatly appreciated.
>
>Best regards,
>
>Katica
>
>
>
>>Dear Katica,
>>
>>
>>there is indeed no reason why stomatal complexes in the petiole should
>>be different from stomatal complexes in leaf lamina seen from the
>>anatomical point of view. The new structure that you propose, is fine.
>>
>>Kind regards,
>>
>>Ruth
>>
>>
>>Katica Ilic wrote:
>>
>>
>>
>>>Dear Ruth,
>>>
>>>Thank you for your reply. It is essential for us at POC to learn how people
>>>
>>>
>use
>
>
>>>Plant Ontology and what kind of requests and issues they may have once they
>>>
>>>
>get
>
>
>>>familiar with this vocabulary.
>>>
>>>I have another question for you, regarding gene expressions in petiole and
>>>
>>>
>leaf
>
>
>>>lamina. On your mc slides, have you seen any differential expression of
>>>
>>>
>gene(s)
>
>
>>>in the guard cells of petioles vs. guard cells in leaf blade? If you have,
>>>
>>>
>that
>
>
>>>would be an argument for creating two terms, 'stomatal complex of the leaf
>>>lamina' and 'petiole stomatal complex', so that gene x (expressed only in
>>>
>>>
>guard
>
>
>>>cell of the petiole) could be properly associated to term 'petiole stomatal
>>>complex'. I couldn't find any evidence of such cases in the published
>>>literature, so, our ontology group at POC decided not to distinguish between
>>>stomata in the leaf lamina and those in the leaf petiole. Therefore,
>>>
>>>
>>annotation
>>
>>
>>>of the gene expression pattern in guard cells of petiole cannot be
>>>
>>>
>>distinguished
>>>from guard cell in the leaf blade. In the example below, you will see that
>>
>>
>the
>
>
>>>same term (stomatal complex) is propagated under both, 'leaf lamina
>>>
>>>
>epidermis'
>
>
>>>and 'petiole epidermis'. If you think this should be corrected, please let me
>>>know.
>>>
>>>This is the illustration:
>>>leaf
>>> (p) leaf lamina
>>> (i) leaf lamina epidermis
>>> (p) stomatal complex
>>> (i) petiole epidermis
>>> (p) stomatal complex
>>>
>>>The rest of the terms that you requested are now placed under term 'petiole',
>>>although we decided not to include all terms, such as interfascicular
>>>parenchyma, or pith (neither one is part of vascular system). Please, note
>>>
>>>
>>that,
>>
>>
>>>unlike for the term 'stomatal complex', we included specific subclasses of
>>>
>>>
>>terms
>>
>>
>>>'leaf vascular system' and 'leaf epidermis', that is, 'leaf lamina vascular
>>>system' and 'petiole vascular system', and 'leaf lamina epidermis' and
>>>
>>>
>'petiole
>
>
>>>epidermis'. This is dictated by the hierarchical nature of the ontology
>>>structure, and by the annotation display requirements. Again, 'stomatal
>>>
>>>
>>complex'
>>
>>
>>>is an exemption of the rule.
>>>
>>>Here is the new structure (for simplicity, I didn't list all the terms under
>>>'leaf':
>>>
>>> leaf
>>> (p) leaf lamina
>>> (p) leaf lamina epidermis
>>> (p) stomatal complex
>>> (p) leaf lamina vascular system
>>> (p) leaf apex
>>> (p) leaf margin
>>> (p) leaf vein
>>>
>>> (p) petiole
>>> (p) petiole cortex
>>> (p) petiole vascular system
>>> (p) petiole epidermis
>>> (p) stomatal complex
>>>
>>>We are currently experiencing problems with cvs repository, and the new
>>>
>>>
>>ontology
>>
>>
>>>files will not be available to download until the problems are fixed. The
>>>updated ontology will be available on our ontology browser after the next
>>>scheduled update (end of June).
>>>
>>>I hope that this new structure with additional children terms under term
>>>'petiole' will meet your requirements. Please let me know if this would work
>>>
>>>
>>and
>>
>>
>>>don't hesitate to ask me additional questions you may have about plant
>>>ontologies.
>>>
>>>Best regards,
>>>
>>>Katica
>>>
>>>
>>>
>>>
>>>
>>>>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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>--
>>>>==================================================================
>>>>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
>>>>==================================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>--
>>==================================================================
>>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
>>==================================================================
>>
>>
>>
>>
--
==================================================================
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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