SAM restructuring suggestion

[Pankaj Jaiswal]

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
>
>