spatial terms

[Toby Kellogg]

I think we need to think hard about what will be gained or lost by
including terms like first second third leaf.   The conventions on counting
are different in different plants (e.g top down vs. bottom up), and leaves
with the same number may or may not be comparable.  Even among maize
inbreds there is variation in the number of leaves before the
juvenile/adult transition and before flowering.  I'd suggest that such
numbering schemes fall into species-specific ontologies and therefore
should be excluded from the general plant ontology.  Perhaps this is
something we should discuss at our May meeting.
Toby

>Depends on how you are defining the first leaf- doesnt it.
>Counting from first leaf after the cotyledon (which may or may not be
>formed in the embryo prior to dessication)...
>Leonore
>
>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote:
>
>>
>> Hi Everyone,
>>
>> I just now started working on the leaf section and encountered the
>> problem on how do we represent the spatial organization. Since
>> PATO/phenotype attribute ontology is way off from implementation what
>> are our rules on this.
>>
>> here are a few spatial attribute examples which I think are necessary to
>> describe a gene's transcript/protein expression profile or a phenotype.
>>
>>
>> first
>> second
>> third
>> fourth
>> fifth
>> 	e.g.
>> 	first leaf
>> 	second leaf
>> 	first / second internode
>> 	first / second node
>> basal
>> uppermost ; synonym:topmost
>> lower
>> upper
>> 	e.g.
>> 	basal / uppermost internodes
>> 	topmost leaves
>> 	lower floret
>> 	upper floret
>> primary
>> secondary
>> 	e.g.
>> 	primary / secondary panicle branches
>> 	spikelets of the primary branches
>>
>>
>>
>
>-------------------------------------------------------------------------------
>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>The Arabidopsis Information Resource	FAX: (650) 325-6857
>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>Department of Plant Biology		URL: http://arabidopsis.org/
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>Stanford, CA 94305
>-------------------------------------------------------------------------------


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/