SAM restructuring suggestion

Tue Jun 14 15:25:31 EDT 2005

I disagree with Leonore in some aspects and agree that there are 
annotation anomalies. Howevere, if there are genes and phenotypes known 
to be responsible for the biological processes involved in "transition 
of SAM from vegetative to reproductive meristem", I would not simply 
annotate them to flower or inflorescence/.shoot/current SAM term, but 
specifically to the two SAM types. The terms vegetative and reproductive 
apical meristems are current required for annotation.

Here is an example:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42
Plant J. 2002 Mar;29(6):743-50
Overexpression of RCN1 and RCN2, rice TERMINAL FLOWER 1/CENTRORADIALIS 
homologs, confers delay of phase transition and altered panicle 
morphology in rice.
Nakagawa M, Shimamoto K, Kyozuka J.

On historical grounds, many of the Arabidopsis flowering time genes are 
considered homologs (rather orthologs) of the Heading time/inflorescence 
exsertion time genes. By saying heading means the flower is not yet 
ready for flowering (anthesis), whereas in case of Arabidopsis, it is 
often the flowering (anthesis). This is one classical example where one 
can see the inflorescence very early in Arabidopsis plant, compared to 
the much later stage in rice or any other cereal where one looks at the 
inflorescence for the first time at the heading stage. By heading stage 
the inflorescence/flower development is almost complete, except for the 
elongation of the rachis.

-Pankaj

kellogge wrote:

> I agree with Leonore on this - I think flowering time mutants are 
> defective in a process, not in a particular organ, so use of the plant 
> structure ontology is not warranted.
>
> This exchange also brings up the general situation created by deciding 
> that we'll add terms "as needed." Obviously as our knowledge of plants 
> increases, the ontology will have to change. Also, the ontology is has 
> not been extensively tested for annotation yet, and there may prove to 
> be whole sections that don't work and have to be redone. On the other 
> hand, do we want/need to have a protracted email conversation among 10 
> or so people every time an annotator sees the need for a new term? It 
> seems as though it might be useful to have some way to accumulate a 
> list of queries/problems that pertain to a particular node, and then 
> once every 6 months or year, sit down and reassess the entire node. 
> Otherwise, I fear that the attempt at unification will get lost pretty 
> quickly.
>
> Toby
>
> On Jun 10, 2005, at 4:21 PM, Leonore Reiser wrote:
>
>     So Pankaj
>     your suggestion raises a question about annotations that we were
>     discussing here the other day. Are you proposing to annotate the
>     expression of these genes to these body parts or the phenotype of
>     mutant alleles/germplasms to these body parts?
>
>     NASC also has a lot of flowering time mutants annotated- in their
>     case, they annotated to the BODY part -flower-
>     possibly because there was/is not term to reflect
>     vegetative-reproductive stage.  I find that wildly confusing and
>     its not where I would look to find flowering time mutants.
>
>      I would annotate something like Constans or FLC as being INVOLVED
>     IN the biological process of flowering (which  called flower
>     development in the GO). I would not use an annotation to
>     vegetative or reproductive meristem to describe the phenotype.
>
>     I think it is a big mistake to try and use the Plant Ontologies to
>     describe every mutant phenotype- its just not possible. Mutants
>     involved in nitrogen assimilation may be chlorotic (pale green or
>     yellow leaves) but the PO cannot effectively describe say
>     sensitivity to a nitrogen analog.
>     So I may be jumping the gun because this could be totally NOT what
>     you are intending to use these terms for. But if so perhaps we
>     could use this as an example and see how other groups would
>     annotate late or early flowering mutant phenotypes? Its a really
>     good exercise.
>
>
>     Leonore
>
>
>
>     On 6/10/05, Pankaj Jaiswal <pj37 at cornell.edu> wrote:
>
>     <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
>
>
>     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
>
>
>
> Elizabeth A. Kellogg
> E. Desmond Lee and Family Professor of Botanical Studies
> Department of Biology
> University of Missouri-St. Louis
> St. Louis, MO 63121
> Tel: 314-516-6217
> FAX: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.html 
>
>