SAM restructuring suggestion

Tue Jun 14 15:39:31 EDT 2005

Simon
I agree that we need to have some standards defined -thats sorta my main 
objective.Your comment and Pankaj's both highlight the issue of needing to 
annotate and not having the 'right term', either because the term didnt 
exist (like if you wanted to describe a developmental stage using PO terms) 
or because it requires instantiation of something that might (eventually) be 
a combinatiorial term.

So say for Pankaj's case of needing to annotate to a gene being expressed in 
the shoot apical meristem during the vegetative stage of growth- I suppose 
ideally one would want either the combinatorial term or combinatorial 
annotation,but then how long do you wait for the software to exist. Indeed 
one of the reasons why i dont think we should wait 6 months to review 
terms/nodes is precisely for this reason...

My main goal is to stimulate discussion and hopefully come to some basic 
agreements. 'Cause we all probably have had the same questions at some 
point. I have my point of view- but its just that- succeptible to change 
based on discussion/good arguments against and the vagueness of my mind.

Maybe we can meet at the Arabidopsis meeting and talk about Arabidopsis 
annotation (I know you wont be there but if Sean and other s are that would 
be great). 

Leonore

On 6/14/05, Simon Jupp <simon at arabidopsis.info> 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> 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
> > 
> >  
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