spatial terms

[Leonore Reiser]

I agree. For maize, there are well defined plastochron idicies, but from
what I have seen, not so well defined for arabidopsis. And like maize ,
can be quite variable in the number of leaves produced prior to flowering-
especially when the light regime is altered. Maybe the thing to is look at
what sorts of annotations Pankaj is referring to and see how they can be
accomodated. Always helps to have the data at hand.


 On Mon, 22 Mar 2004, Toby Kellogg wrote:

> 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/
> >260 Panama St.
> >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/
>
>

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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/
260 Panama St.
Stanford, CA 94305
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