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<font size="-1">Hi,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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. <br>
<br>
Simon<br>
NASC<br>
<br>
<br>
<br>
</font><br>
<br>
<blockquote cite="mid248c981f05061015543a2ce2bf@mail.gmail.com"
type="cite">Pankaj<br>
<br>
Now that there are terms that define stages of plant development- could
these mutants be annotated to 'reproductive stage'<br>
so in PATOese<br>
that might be something like <br>
entity:reproductive stage<br>
attribute: timing<br>
value: early or late?<br>
<br>
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.<br>
<br>
Leonore<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>
</blockquote>
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