spatial terms
Vincent, Leszek
Leszek at missouri.edu
Tue Mar 23 14:15:12 EST 2004
Colleagues,
Leonore's question is very relevant ('how many genes are currently
annotated to a specific internode?') for it cites the need to annotate
genes to 'body parts' e.g. internodes. Pankaj's comments about rice leaf
position (top down counting) & Toby's comments about 'sensu...' being
cumbersome & the suggestion that "such numbering schemes fall into
species-specific ontologies and therefore should be excluded from the
general plant ontology." - and Sue's counter to the latter point. And
Pankaj's comments: "I think this issue will keep coming up every now and
then, because at Gramene we do not want to maintain two different
ontology sets. I guess
the same goes with TAIR and MaizeGDB. A generic one from POC and
species specific from our own databases. This is too much of work and
was also the main reason why we wanted to have this project." All these
perspectives point to our wrestling with how to incorporate the complex
diversity of plant structure into a general/composite plant ontology. OK
- nothing new here - but please consider the following contribution.
This is an important discussion because it again points to the
sophistication of the foundation upon which we are building the PO which
in turn will probably determine the acceptance (or otherwise) of the PO
controlled vocabulary by the plant science community. Having a single
plant ontology which accommodates the needed diversity of plant
structure for many taxa vs a simplified (consensus) ontology & separate
species specific ontologies are two rather different paradigms. My
understanding of the mandate of the POC is that it was focusing on the
former & not the latter. Am I wrong? Why does it seem to be a stumbling
block to include taxon-specific plant structure vocabulary (where
needed) in our PO product? I look forward to discussing this matter
further (at the May meeting - hopefully before then).
- Leszek
-------
Optional reading: A little detail on the complexity of leaf position
nomenclature for Zea mays:
In maize (Zea mays a member of the grass family, Poaceae) there appear
to be 2 'nomenclatures' that are used: 1. Juvenile leaves vs adult
leaves 2. Leaf Number (L), counting the non-leaf coleoptile as zero and
Plastochron Number (P), counting the established but predivision
meristematic founder cells as zero (complex? rather!). Toby mentioned
the first system in her earlier email.
The second system may seem more tricky than the first BUT there's some
counter-intuition in the first system. How? Well, the term "Juvenile
leaves" has a distinct developmental tag in that juvenile leaves arise
earlier and in a more basal position than the younger, more adult leaves
(quoting from Freeling & Lane, Ch3 in The Maize Handbook). In MaizeGDB
there are 10,708 ESTs associated with 'juvenile leaf' & 8,789 ESTs
associated with adult tissue (incl. adult leaves). At present MaizeGDB
is not using explicitly using a leaf number system, counting from the
bottom up, but this is implicit in the use of juvenile & adult leaves.
Using the L & P convention, L10, P3 would be referring to the tenth leaf
above the coleoptile when the leaf is the third leaf from the meristem
(a leaf at approx. 4 mm primordial devel. stage). There are a few
publications using the L & P nomenclature but no use of it (YET) in
MaizeGDB.
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit
Dept. of Agronomy
215 Curtis Hall
University of Missouri-Columbia
Columbia
MO 65211-7020
USA
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850
Email: Leszek at missouri.edu
Plant Systematist on The Plant Ontology Consortium - NSF award 0321666
Associate Curator, Dunn-Palmer Herbarium (UMO)
Research Associate, Missouri Botanical Garden (MO), USA
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Roger Wise
> Sent: Monday, March 22, 2004 3:27 PM
> To: po-dev at plantontology.org
> Subject: Re: spatial terms
>
>
> It seems to make sense to me to count from the bottom, because in
> many global expression studies, tissue is harvested, or dissected,
> before maturity. It is also important to have these stages
> well-defined, possibly species specific, because, again, in global
> expression studies, hundreds of genes are differentially expressed
> between specific stages or tissues (including anthers from upper and
> lower florets). At least for this particular application, and in the
> foreseeable future (eg. laser capture) more detail is better. As for
> cultivar differences, this should be defined by stating the cultivar
> along with the definition.
>
> Roger
>
> At 2:05 PM -0500 3/22/04, Toby Kellogg wrote:
> >I think maize counts from the bottom. so at a minimu we'd
> have to say
> >"internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty
> >cumbersome to me. Leonore's question is probably the most
> relevant -
> >how many genes are currently annotated to a specific internode? Toby
> >
> >>Toby Kellogg wrote:
> >>> I think we need to think hard about what will be gained
> or lost by
> >>> including terms like first second third leaf. The
> conventions on counting
> >>> are different in different plants (e.g top down vs.
> bottom up), and
> >>> leaves with the same number may or may not be comparable. Even
> >>> among maize inbreds there is variation in the number of leaves
> >>> before the juvenile/adult transition and before flowering. I'd
> >>> suggest that such numbering schemes fall into species-specific
> >>> ontologies and therefore should be excluded from the
> general plant
> >>> ontology. Perhaps this is something we should discuss
> at our May
> >>> meeting. Toby
> >>>
> >>
> >>I agree with Leonore and Toby on how you count the numbers and how
> >>many numbers, based on the germplasm/variety/population
> type and the
> >>species. Looks like we need to comeup with a solution soon.
> I know in
> >>majority of the rice reports the counts are from the top, because
> >>often researchers do not see the 1st and 2nd internode/node.
> >>
> >>To make things simple we can always say that gene-x is expressed in
> >>internode. But then we loose the granularity we want to
> suggest to our
> >>user that look the gene is expressed in Second internode
> ONLY. This is
> >>different than assigning it to the generic term internode.
> >>
> >>I think this issue will keep coming up every now and then,
> because at
> >>Gramene we do not want to maintain two different ontology sets. I
> >>guess the same goes with TAIR and MaizeGDB. A generic one from POC
> >>and species specific from our own databases. This is too
> much of work
> >>and was also the main reason why we wanted to have this project.
> >>
> >>Pankaj
> >>
> >>
> >>>
> >>>>Depends on how you are defining the first leaf- doesnt
> it. Counting
> >>>>from first leaf after the cotyledon (which may or may not
> be formed
> >>>>in the embryo prior to dessication)... Leonore
> >>>>
> >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote:
> >>>>
> >>>>
> >>>>>Hi Everyone,
> >>>>>
> >>>>>I just now started working on the leaf section and
> encountered the
> >>>>>problem on how do we represent the spatial organization. Since
> >>>>>PATO/phenotype attribute ontology is way off from implementation
> >>>>>what are our rules on this.
> >>>>>
> >>>>>here are a few spatial attribute examples which I think are
> >>>>>necessary to describe a gene's transcript/protein expression
> >>>>>profile or a phenotype.
> >>>>>
> >>>>>
> >>>>>first
> >>>>>second
> >>>>>third
> >>>>>fourth
> >>>>>fifth
> >>>>> e.g.
> >>>>> first leaf
> >>>>> second leaf
> >>>>> first / second internode
> >>>>> first / second node
> >>>>>basal
> >>>>>uppermost ; synonym:topmost
> >>>>>lower
> >>>>>upper
> >>>>> e.g.
> >>>>> basal / uppermost internodes
> >>>>> topmost leaves
> >>>>> lower floret
> >>>>> upper floret
> >>>>>primary
> >>>>>secondary
> >>>>> e.g.
> >>>>> primary / secondary panicle branches
> >>>>> spikelets of the primary branches
> >>>>>
> >>>>>
> >
> >
> >Elizabeth A. Kellogg
> >Department of Biology
> >University of Missouri-St. Louis
> >8001 Natural Bridge Road
> >St. Louis, MO 63121
> >phone: 314-516-6217
> >fax: 314-516-6233
> >http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
>
> --
> _____________________________
> Roger Wise, USDA-ARS
> Department of Plant Pathology
> 411 Bessey Hall
> Iowa State University, Ames, IA
> 50011-1020 USA
> Phone: 515-294-9756
> Fax: 515-294-9420
> E-mail: rpwise at iastate.edu
> _____________________________
> http://wiselab.org/
> http://barleybase.org/
> http://www.plantstress.iastate.edu/
>
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