Feedback on POC: granular terms under 'petiole' (PR#56)
Katica Ilic
jitterbug at plantontology.org
Tue May 31 16:39:18 EDT 2005
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
> ==================================================================
>
>
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