spatial terms
Peter Stevens
peter.stevens at mobot.org
Tue Mar 23 15:09:41 EST 2004
>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 without needing a translator. Our chaotic terminology is
>one of the major taxonomic impediments, to say nothing of other
>problems it causes..
Peter S.
>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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