SAM restructuring suggestion

[Pankaj Jaiswal]

Rather fortunately, in this example we do know it,  based on the 
experimental designs and phenotypic analyses. The two rice genes are 
putative orthologs of  TFL1.

-Pankaj

Leonore Reiser wrote:

> 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 
> <mailto: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
>     <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>
>     > <mailto: 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>
>     >     <
>     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>
>     >     <
>     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
>     >
>     >
>
>