SAM restructuring suggestion

[kellogge]

I agree with Leonore on this - I think flowering time mutants are  
defective in a process, not in a particular organ, so use of the plant  
structure ontology is not warranted.

This exchange also brings up the general situation created by deciding  
that we'll add terms "as needed."  Obviously as our knowledge of plants  
increases, the ontology will have to change.  Also, the ontology is has  
not been extensively tested for annotation yet, and there may prove to  
be whole sections that don't work and have to be redone.  On the other  
hand, do we want/need to have a protracted email conversation among 10  
or so people every time an annotator sees the need for a new term?  It  
seems as though it might be useful to have some way to accumulate a  
list of queries/problems that pertain to a particular node, and then  
once every 6 months or year, sit down and reassess the entire node.   
Otherwise, I fear that the attempt at unification will get lost pretty  
quickly.

Toby

On Jun 10, 2005, at 4:21 PM, Leonore Reiser wrote:

> 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&qu 
> ery=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
>
>
>
Elizabeth A. Kellogg
E. Desmond Lee and Family Professor of Botanical Studies
Department of Biology
University of Missouri-St. Louis
St. Louis, MO 63121
Tel: 314-516-6217
FAX: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ 
home.html
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