SAM restructuring suggestion

[Leonore Reiser]

i agree- you dont really know what stage is affected.
thats why I think a more accurate term is the process term not a body part 
or stage.

On 6/14/05, Pankaj Jaiswal <pj37 at cornell.edu> wrote:
> 
> Once again this is a curation anomaly like whether the glass is half
> empty or half full. A curator can instead say that
> 
> entity:vegetative stage
> attribute: phase/length
> value: extended
> 
> In this paper
> 
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42
> The RCN1/2 overexpression can give a severe phenotype with no-heading.
> Means the plant never reached the vegetative phase. Then what?
> 
> entity:reproductive stage
> attribute: timing
> value: absent??
> 
> Or may require two annotations
> 
> entity:vegetative stage
> attribute: phase/length
> value: extended
> 
> entity:reproductive stage
> attribute: timing
> value: delayed/absent??
> 
> In any case Gramene is not doing the EAV type annotations for the
> moment, though we intend to do it sometime next year.
> 
> -Pankaj
> 
> 
> Leonore Reiser wrote:
> 
> > Pankaj
> >
> > Now that there are terms that define stages of plant development-
> > could these mutants be annotated to 'reproductive stage'
> > so in PATOese
> > that might be something like
> > entity:reproductive stage
> > attribute: timing
> > value: early or late?
> >
> > Ill hopefully get a chance to talk to Sean May from NASC at the
> > Arabidopsis meeting and see what he thinks about their annotations as
> > well and maybe compare notes on flowering time mutant annotation.
> >
> > Leonore
> >
> >
> > On 6/10/05, Pankaj Jaiswal <pj37 at cornell.edu
> > <mailto:pj37 at cornell.edu>> wrote:
> >
> >
> > <
> http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482
> > <
> 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
> > <
> 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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