spatial terms

[Roger Wise]

It seems to make sense to me to count from the bottom, because in 
many global expression studies, tissue is harvested, or dissected, 
before maturity.  It is also important to have these stages 
well-defined, possibly species specific, because, again, in global 
expression studies, hundreds of genes are differentially expressed 
between specific stages or tissues (including anthers from upper and 
lower florets).  At least for this particular application, and in the 
foreseeable future (eg. laser capture) more detail is better.  As for 
cultivar differences, this should be defined by stating the cultivar 
along with the definition.

Roger

At 2:05 PM -0500 3/22/04, 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
>
>>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/


-- 
_____________________________
Roger Wise, USDA-ARS
Department of Plant Pathology
411 Bessey Hall
Iowa State University, Ames, IA 
50011-1020  USA
Phone:  515-294-9756
Fax:    515-294-9420
E-mail: rpwise at iastate.edu
_____________________________
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