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<blockquote type="cite" cite>I thought the general point of this whole
operation was to have a general onotology so that indeed different
people can talk to one another<u> without</u> needing a
translator. Our chaotic terminology is one of the major
taxonomic impediments, to say nothing of other problems it
causes..</blockquote>
<div><br>
<br>
</div>
<div>Peter S.<br>
</div>
<blockquote type="cite" cite>Colleagues,<br>
<br>
Leonore's question is very relevant ('how many genes are currently<br>
annotated to a specific internode?') for it cites the need to
annotate<br>
genes to 'body parts' e.g. internodes. Pankaj's comments about rice
leaf<br>
position (top down counting) & Toby's comments about 'sensu...'
being<br>
cumbersome & the suggestion that "such numbering schemes
fall into<br>
species-specific ontologies and therefore should be excluded from
the<br>
general plant ontology." - and Sue's counter to the latter
point. And<br>
Pankaj's comments: "I think this issue will keep coming up every
now and<br>
then, because at Gramene we do not want to maintain two different<br>
ontology sets. I guess<br>
the same goes with TAIR and MaizeGDB. A generic one from POC
and<br>
species specific from our own databases. This is too much of work
and<br>
was also the main reason why we wanted to have this project."
All these<br>
perspectives point to our wrestling with how to incorporate the
complex<br>
diversity of plant structure into a general/composite plant ontology.
OK<br>
- nothing new here - but please consider the following
contribution.<br>
<br>
This is an important discussion because it again points to the<br>
sophistication of the foundation upon which we are building the PO
which<br>
in turn will probably determine the acceptance (or otherwise) of the
PO<br>
controlled vocabulary by the plant science community. Having a
single<br>
plant ontology which accommodates the needed diversity of plant<br>
structure for many taxa vs a simplified (consensus) ontology &
separate<br>
species specific ontologies are two rather different paradigms. My<br>
understanding of the mandate of the POC is that it was focusing on
the<br>
former & not the latter. Am I wrong? Why does it seem to be a
stumbling<br>
block to include taxon-specific plant structure vocabulary (where<br>
needed) in our PO product? I look forward to discussing this
matter<br>
further (at the May meeting - hopefully before then).<br>
<br>
- Leszek<br>
-------<br>
Optional reading: A little detail on the complexity of leaf
position<br>
nomenclature for Zea mays:<br>
<br>
In maize (Zea mays a member of the grass family, Poaceae) there
appear<br>
to be 2 'nomenclatures' that are used: 1. Juvenile leaves vs adult<br>
leaves 2. Leaf Number (L), counting the non-leaf coleoptile as
zero and<br>
Plastochron Number (P), counting the established but predivision<br>
meristematic founder cells as zero (complex? rather!). Toby
mentioned<br>
the first system in her earlier email.<br>
<br>
The second system may seem more tricky than the first BUT there's
some<br>
counter-intuition in the first system. How? Well, the term
"Juvenile<br>
leaves" has a distinct developmental tag in that juvenile leaves
arise<br>
earlier and in a more basal position than the younger, more adult
leaves<br>
(quoting from Freeling & Lane, Ch3 in The Maize Handbook). In
MaizeGDB<br>
there are 10,708 ESTs associated with 'juvenile leaf' & 8,789
ESTs<br>
associated with adult tissue (incl. adult leaves). At present
MaizeGDB<br>
is not using explicitly using a leaf number system, counting from
the<br>
bottom up, but this is implicit in the use of juvenile & adult
leaves.<br>
<br>
Using the L & P convention, L10, P3 would be referring to the
tenth leaf<br>
above the coleoptile when the leaf is the third leaf from the
meristem<br>
(a leaf at approx. 4 mm primordial devel. stage). There are a few<br>
publications using the L & P nomenclature but no use of it (YET)
in<br>
MaizeGDB.<br>
<br>
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*<br>
P. Leszek D. Vincent Ph.D., FLS<br>
Plant Science Unit<br>
Dept. of Agronomy<br>
215 Curtis Hall<br>
University of Missouri-Columbia<br>
Columbia<br>
MO 65211-7020<br>
USA<br>
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850<br>
Email: Leszek@missouri.edu<br>
Plant Systematist on The Plant Ontology Consortium - NSF award
0321666<br>
Associate Curator, Dunn-Palmer Herbarium (UMO)</blockquote>
<blockquote type="cite" cite>Research Associate, Missouri Botanical
Garden (MO), USA<br>
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*<br>
<br>
> -----Original Message-----<br>
> From: owner-po-dev@brie4.cshl.org<br>
> [mailto:owner-po-dev@brie4.cshl.org] On Behalf Of Roger Wise<br>
> Sent: Monday, March 22, 2004 3:27 PM<br>
> To: po-dev@plantontology.org<br>
> Subject: Re: spatial terms<br>
><br>
><br>
> It seems to make sense to me to count from the bottom, because
in<br>
> many global expression studies, tissue is harvested, or
dissected,<br>
> before maturity. It is also important to have these
stages<br>
> well-defined, possibly species specific, because, again, in
global<br>
> expression studies, hundreds of genes are differentially
expressed<br>
> between specific stages or tissues (including anthers from upper
and<br>
> lower florets). At least for this particular application,
and in the<br>
> foreseeable future (eg. laser capture) more detail is
better. As for<br>
> cultivar differences, this should be defined by stating the
cultivar<br>
> along with the definition.<br>
><br>
> Roger<br>
><br>
> At 2:05 PM -0500 3/22/04, Toby Kellogg wrote:<br>
> >I think maize counts from the bottom. so at a minimu
we'd<br>
> have to say<br>
> >"internode 3 sensu maize" or "internode 3
sensu rice". Seems pretty<br>
> >cumbersome to me. Leonore's question is probably the
most<br>
> relevant -<br>
> >how many genes are currently annotated to a specific
internode? Toby<br>
> ><br>
> >>Toby Kellogg wrote:<br>
> >>> I think we need to think hard about what will
be gained<br>
> or lost by<br>
> >>> including terms like first second third
leaf. The<br>
> conventions on counting<br>
> >>> are different in different plants (e.g top
down vs.<br>
> bottom up), and<br>
> >>> leaves with the same number may or may not be
comparable. Even<br>
> >>> among maize inbreds there is variation in the
number of leaves<br>
> >>> before the juvenile/adult transition and
before flowering. I'd<br>
> >>> suggest that such numbering schemes fall into
species-specific<br>
> >>> ontologies and therefore should be excluded
from the<br>
> general plant<br>
> >>> ontology. Perhaps this is something we
should discuss<br>
> at our May<br>
> >>> meeting. Toby<br>
> >>><br>
> >><br>
> >>I agree with Leonore and Toby on how you count the
numbers and how<br>
> >>many numbers, based on the
germplasm/variety/population<br>
> type and the<br>
> >>species. Looks like we need to comeup with a solution
soon.<br>
> I know in<br>
> >>majority of the rice reports the counts are from the
top, because<br>
> >>often researchers do not see the 1st and 2nd
internode/node.<br>
> >><br>
> >>To make things simple we can always say that gene-x is
expressed in<br>
> >>internode. But then we loose the granularity we want
to<br>
> suggest to our<br>
> >>user that look the gene is expressed in Second
internode<br>
> ONLY. This is<br>
> >>different than assigning it to the generic term
internode.<br>
> >><br>
> >>I think this issue will keep coming up every now and
then,<br>
> because at<br>
> >>Gramene we do not want to maintain two different
ontology sets. I<br>
> >>guess the same goes with TAIR and MaizeGDB. A generic
one from POC<br>
> >>and species specific from our own databases. This is
too<br>
> much of work<br>
> >>and was also the main reason why we wanted to have this
project.<br>
> >><br>
> >>Pankaj<br>
> >><br>
> >><br>
> >>><br>
> >>>>Depends on how you are defining the first leaf-
doesnt<br>
> it. Counting<br>
> >>>>from first leaf after the cotyledon (which may
or may not<br>
> be formed<br>
> >>>>in the embryo prior to dessication)...
Leonore<br>
> >>>><br>
> >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote:<br>
> >>>><br>
> >>>><br>
> >>>>>Hi Everyone,<br>
> >>>>><br>
> >>>>>I just now started working on the leaf
section and<br>
> encountered the<br>
> >>>>>problem on how do we represent the spatial
organization. Since<br>
> >>>>>PATO/phenotype attribute ontology is way off
from implementation<br>
> >>>>>what are our rules on this.<br>
> >>>>><br>
> >>>>>here are a few spatial attribute examples
which I think are<br>
> >>>>>necessary to describe a gene's
transcript/protein expression<br>
> >>>>>profile or a phenotype.<br>
> >>>>><br>
> >>>>><br>
> >>>>>first<br>
> >>>>>second<br>
> >>>>>third<br>
> >>>>>fourth<br>
> >>>>>fifth<br>
> >>>>><x-tab>
</x-tab>e.g.<br>
> >>>>><x-tab>
</x-tab>first leaf<br>
> >>>>><x-tab>
</x-tab>second leaf<br>
> >>>>><x-tab>
</x-tab>first / second internode<br>
> >>>>><x-tab> </x-tab>first / second node<br>
> >>>>>basal<br>
> >>>>>uppermost ; synonym:topmost<br>
> >>>>>lower</blockquote>
<blockquote type="cite" cite>> >>>>>upper<br>
> >>>>><x-tab>
</x-tab>e.g.<br>
> >>>>><x-tab>
</x-tab>basal / uppermost internodes<br>
> >>>>><x-tab>
</x-tab>topmost leaves<br>
> >>>>><x-tab> </x-tab>lower floret<br>
> >>>>><x-tab>
</x-tab>upper floret<br>
> >>>>>primary<br>
> >>>>>secondary<br>
> >>>>><x-tab>
</x-tab>e.g.<br>
> >>>>><x-tab>
</x-tab>primary / secondary panicle branches<br>
> >>>>><x-tab>
</x-tab>spikelets of the primary branches<br>
> >>>>><br>
> >>>>><br>
> ><br>
> ><br>
> >Elizabeth A. Kellogg<br>
> >Department of Biology<br>
> >University of Missouri-St. Louis<br>
> >8001 Natural Bridge Road<br>
> >St. Louis, MO 63121<br>
> >phone: 314-516-6217<br>
> >fax: 314-516-6233<br>
> >http://www.umsl.edu/divisions/artscienc<span
></span>e/biology/Kellogg/Kellogg/<br>
><br>
><br>
> --<br>
> _____________________________<br>
> Roger Wise, USDA-ARS<br>
> Department of Plant Pathology<br>
> 411 Bessey Hall<br>
> Iowa State University, Ames, IA<br>
> 50011-1020 USA<br>
> Phone: 515-294-9756<br>
> Fax: 515-294-9420<br>
> E-mail: rpwise@iastate.edu<br>
> _____________________________<br>
> http://wiselab.org/<br>
> http://barleybase.org/<br>
> http://www.plantstress.iastate.edu/<br>
></blockquote>
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