SAM restructuring suggestion

[Leonore Reiser]

So Pankaj
your suggestion raises a question about annotations that we were discussing 
here the other day. Are you proposing to annotate the expression of these 
genes to these body parts or the phenotype of mutant alleles/germplasms to 
these body parts?

NASC also has a lot of flowering time mutants annotated- in their case, they 
annotated to the BODY part -flower-
possibly because there was/is not term to reflect vegetative-reproductive 
stage. I find that wildly confusing and its not where I would look to find 
flowering time mutants.

I would annotate something like Constans or FLC as being INVOLVED IN the 
biological process of flowering (which called flower development in the GO). 
I would not use an annotation to vegetative or reproductive meristem to 
describe the phenotype.

I think it is a big mistake to try and use the Plant Ontologies to describe 
every mutant phenotype- its just not possible. Mutants involved in nitrogen 
assimilation may be chlorotic (pale green or yellow leaves) but the PO 
cannot effectively describe say sensitivity to a nitrogen analog.
So I may be jumping the gun because this could be totally NOT what you are 
intending to use these terms for. But if so perhaps we could use this as an 
example and see how other groups would annotate late or early flowering 
mutant phenotypes? Its a really good exercise.


Leonore



On 6/10/05, Pankaj Jaiswal <pj37 at cornell.edu> wrote:
> 
> 
> <
> http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482
> >
> 
> 
> Refer to:
> 
> http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148
> 
> Looks like we need a specific instance of SAM, ie. "vegetative shoot
> apical meristem". The current term is too generic for curating
> vegetative SAM.
> 
> The reason being, I am curating a lot of flowering time genes and many
> are involved in regulating the transition of vegetative SAM to
> reproductive SAM. This event is critical in short-day or long-day light
> response resulting in early/delayed flowering.
> 
> Current structure is like follows:
> 
> 
> # PO:0020148 : shoot apical meristem ( 32 )
> 
> * PO:0000224 : central zone
> * PO:0006362 : embryonic shoot apical meristem
> * PO:0000229 : floral meristem
> * PO:0000230 : inflorescence meristem
> * PO:0009020 : meristem L1
> * PO:0009021 : meristem L2
> * PO:0009022 : meristem L3
> * PO:0000225 : peripheral zone
> * PO:0005039 : primary thickening meristem
> * PO:0000226 : rib zone
> * PO:0006306 : shoot procambium
> --------------------------------------------------
> 
> Proposed
> 
> # PO:0020148 : shoot apical meristem ( 32 )
> i PO:new : vegetative shoot apical meristem
> p PO:0000224 : central zone
> i PO:0006362 : embryonic shoot apical meristem
> p PO:0009020 : meristem L1
> p PO:0009021 : meristem L2
> p PO:0009022 : meristem L3
> p PO:0000225 : peripheral zone
> p PO:0005039 : primary thickening meristem
> p PO:0000226 : rib zone
> p PO:0006306 : shoot procambium
> i PO:new : reproductive shoot apical meristem
> i PO:0000229 : floral meristem
> i PO:0000230 : inflorescence meristem
> 
> 
> PO:0020148 : shoot apical meristem
> Def: current
> Meristem formed in the apex of the shoot, including meristems
> originating as axillary shoot meristems.
> Def: proposed
> Meristem formed in the apex of the shoot or those originating as
> axillary and reproductive meristems.
> 
> PO:new : vegetative shoot apical meristem
> Def: proposed
> Copy the original SAM definition.
> 
> PO:new : reproductive shoot apical meristem
> Def: proposed
> Meristem formed in the apex of the shoot originating as
> inflorescence and or flower meristems.
> 
> -Pankaj
> 
>
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