So Pankaj<br>
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?<br>
<br>
NASC also has a lot of flowering time mutants annotated- in their case, they annotated to the BODY part -flower-<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
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.<br>
<br>
<br>
Leonore<br>
<br>
<br>
<br><div><span class="gmail_quote">On 6/10/05, <b class="gmail_sendername">Pankaj Jaiswal</b> <<a href="mailto:pj37@cornell.edu">pj37@cornell.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br><<a href="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
</a>><br><br><br>Refer to:<br><a href="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
</a><br><br>Looks like we need a specific instance of SAM, ie. "vegetative shoot<br>apical meristem". The current term is too generic for curating<br>vegetative SAM.<br><br>The reason being, I am curating a lot of flowering time genes and many
<br>are involved in regulating the transition of vegetative SAM to<br>reproductive SAM. This event is critical in short-day or long-day light<br>response resulting in early/delayed flowering.<br><br>Current structure is like follows:
<br><br><br># PO:0020148 : shoot apical meristem ( 32 )<br><br> * PO:0000224 : central zone<br> * PO:0006362 : embryonic shoot apical meristem<br> * PO:0000229 : floral meristem<br> * PO:0000230 : inflorescence meristem
<br> * PO:0009020 : meristem L1<br> * PO:0009021 : meristem L2<br> * PO:0009022 : meristem L3<br> * PO:0000225 : peripheral zone<br> * PO:0005039 : primary thickening meristem<br> * PO:0000226 : rib zone
<br> * PO:0006306 : shoot procambium<br>--------------------------------------------------<br><br>Proposed<br><br># PO:0020148 : shoot apical meristem ( 32 )<br> i PO:new : vegetative shoot apical meristem<br> p PO:0000224 : central zone
<br> i PO:0006362 : embryonic shoot apical meristem<br> p PO:0009020 : meristem L1<br> p PO:0009021 : meristem L2<br> p PO:0009022 : meristem L3<br> p PO:0000225 : peripheral zone<br> p PO:0005039 : primary thickening meristem
<br> p PO:0000226 : rib zone<br> p PO:0006306 : shoot procambium<br> i PO:new : reproductive shoot apical meristem<br> i PO:0000229 : floral meristem<br> i PO:0000230 : inflorescence meristem<br><br><br>
PO:0020148 : shoot apical meristem<br>Def: current<br> Meristem formed in the apex of the shoot, including meristems<br>originating as axillary shoot meristems.<br>Def: proposed<br> Meristem formed in the apex of the shoot or those originating as
<br>axillary and reproductive meristems.<br><br>PO:new : vegetative shoot apical meristem<br>Def: proposed<br> Copy the original SAM definition.<br><br>PO:new : reproductive shoot apical meristem<br>Def: proposed<br>
Meristem formed in the apex of the shoot originating as<br>inflorescence and or flower meristems.<br><br>-Pankaj<br><br></blockquote></div><br>