spatial terms

[Pankaj Jaiswal]

Some more
http://www.plantcell.org/cgi/content/full/12/9/1591

Pankaj

Pankaj Jaiswal wrote:

> 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
*****************************