spatial terms

[Toby Kellogg]

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/