SAM restructuring suggestion

[Pankaj Jaiswal]

I will talk about the phenotypes in my other mails.

-Pankaj

Simon Jupp wrote:

> Hi,
>
> NASC have been using a combination of PO and PATO terms. In the 
> example you mention we would use a combination to say flower (PO) and 
> late /early (PATO).  If a user is interested in flower mutants, or 
> comes to our site with the flower  PO term they will get a list of 
> attributes from PATO that have been used with the flower term, they 
> can then use these to search the germplasm database.  By doing PO/PATO 
> annotations users have the best chance of finding germplasm with 
> phenotypes they are interested in, it is already proving more powerful 
> than our basic text search function.
>
> We have countless examples where PO/PATO annotations for phenotypes 
> are not true reflections of the phenotypes  being explained by the 
> donor, but we decided we would annotate them the best we could to at 
> least capture the keywords being observed.  Our primary goal is to aid 
> users in searching our database, so we have often over annotated some 
> of our lines.  As there was (is) no standard for doing these 
> annotation we decided to carry on regardless with a view publicise the 
> ontologies to our user base and with a view to refining the 
> annotations later when standards come in place and PATO matures.
>
> I have been waiting for interest  in phenotype annotations to pick up, 
> we have over 1500 mutant phenotypes annotated with PO and PATO terms 
> and would appreciate any feedback from the community on the annotations. 
>
> Simon
> NASC
>
>
>
>
>
>> 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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