spatial terms

[Pankaj Jaiswal]

Here is an example. The example I gave you is somewhat similar.

http://www.pnas.org/cgi/content/full/97/21/11638/F4

pankaj

Leonore Reiser wrote:

> 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
>>*****************************
>>
>>
> 
> 
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------
> 
> 

-- 
******************************
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
*****************************