spatial terms

[Leonore Reiser]

Maybe it would help to have a description or two to look at? Do they say
things like ONLY EXPRESSED IN THE FOURTH INTERNODE?


On Mon, 22 Mar 2004, Pankaj Jaiswal wrote:

>
>
> Toby Kellogg wrote:
>
> > I think maize counts from the bottom.  so at a minimu we'd have to say
> > "internode 3 sensu maize" or "internode 3 sensu rice".   Seems pretty
> > cumbersome to me.  Leonore's question is probably the most relevant - how
> > many genes are currently annotated to a specific internode?
> > Toby
> >
> About 5-6 sequenced genes and 40 classical genes identified by
> phenotype. Rice does not have may sequenced genes with expression
> profile. This trend has just picked up and is much more focussed on the
> parts with agronomic value (stem, seed, panicle).
>
> Pankaj
>
>
> >
> >>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
> >>>
> >>
> >>I agree with Leonore and Toby on how you count the numbers and how many
> >>numbers, based on the germplasm/variety/population type and the species.
> >>Looks like we need to comeup with a solution soon. I know in majority of
> >>the rice reports the counts are from the top, because often researchers
> >>do not see the 1st and 2nd internode/node.
> >>
> >>To make things simple we can always say that gene-x is expressed in
> >>internode. But then we loose the granularity we want to suggest to our
> >>user that look the gene is expressed in Second internode ONLY. This is
> >>different than assigning it to the generic term internode.
> >>
> >>I think this issue will keep coming up every now and then, because at
> >>Gramene we do not want to maintain two different ontology sets. I guess
> >>the same goes with TAIR and MaizeGDB. A generic one  from POC and
> >>species specific from our own databases. This is too much of work and
> >>was also the main reason why we wanted to have this project.
> >>
> >>Pankaj
> >>
> >>
> >>
> >>>>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
> >>>>>
> >>>>>
> >
> >
> >
> > 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/
> >
> >
> >
>
> --
> ******************************
> Pankaj Jaiswal, PhD
> Gramene Database
> Department of Plant Breeding
> G-15 Bradfield Hall
> Cornell University
> Ithaca, NY-14853
>
> tel: +1-607-255-3103
> fax: +1-607-255-6683
> web: http://www.gramene.org
> *****************************
>
>

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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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