SAM restructuring suggestion

[Pankaj Jaiswal]

Sorry
In the RCN1/2 eaxmple
The plants with  severe phenotype showed  no-heading. Means the plant 
never reached the REPRODUCTIVE  phase.

-Pankaj


Pankaj Jaiswal 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
>>
>>
>
>