POC observations so far

Toby Kellogg kellogge at msx.umsl.edu
Fri Oct 3 19:05:45 EDT 2003 

I think we're all converging on a similar solution, and perhaps we could do
with two sibling terms:
gynoecium primordium
gynoecium mature
Then ovary/style/stigma would be part of gynoecium mature.
For the expression domain of tasselseed2, it would be Anatomy location:
gynoecium primordium, dev. stage: aborted gynoecium development.
to be continued...
Toby

>No- it was bad shorthand (and I think what Toby was referring to with
>respect to aborted gynoecium vs. aborted).
>There were 3 instances of gynoecium: gynoecium primordium,
>aborted(rudimentary) gynoecium and mature gynoecium. These were all
>sibling terms right?
>Leonore
>
>On Fri, 3 Oct 2003, Pankaj Jaiswal wrote:
>
>>  >>gynoecium
>>  >>-%gynoecium primordium
>>  >>-%aborted
>>  >>-%mature
>>  >>--<ovary
>>  >>--<stigma
>>  >>--<style
>>
>> Are you suggesting that ovary /style/stigma are PARTOF mature primordium?
>>
>> I think the annotations of any gene product with an expression in this
>> imperfect gynoecium should be annotated for
>> Anatomy Location: rudimentary gynoecium
>> dev. stage: aborted gynoecium development.
>>
>> This stage can be child of Gynoecium development in dev. stage ontology.
>>and a
>> part of any species specific growth stage ontology.
>>
>> Pankaj
>>
>> Toby Kellogg wrote:
>>
>> > That would also be a good possibility - it's sort of an expanded and
>> > slightly more precise version of Pankaj's "rudimentary" category.   A
>> > trivial question:  does the word "gynoecium" need to follow "aborted" and
>> > "mature", or is it understood?
>> > Toby
>> >
>> >
>> >>In a way- what seems to be a solution is stages of development of an organ
>> >>as being instances of an organ (e.g gynoecium primordia is an instance of
>> >>gynoecium), aborted/rudimentary as other instances- so you have a node for
>> >>gynoecium that includes all instances (stages)
>> >>
>> >>gynoecium
>> >>-%gynoecium primordium
>> >>-%aborted
>> >>-%mature
>> >>--<ovary
>> >>--<stigma
>> >>--<style
>> >>
>> >>not being comprehensive here but this is the general picture.
>> >>Leonore
>> >>
>> >>
>> >>On Fri, 3 Oct 2003, Toby Kellogg wrote:
>> >>
>> >>
>> >>>Just a simultaneous addition to Felipe's comment:
>> >>>Unisexual flowers are pretty common in Poaceae and in angiosperms in
>> >>>general.  Among model systems they occur in Populus, sugar beet, Silene,
>> >>>and the outer florets of some sunflower relatives, so if we can solve the
>> >>>problem for maize, we will have solved a number of similar problems.  The
>> >>>difficulty is that in maize, as in many angiosperms, all flowers start
>> >>>development as bisexual structures; in staminate florets, the pistil then
>> >>>aborts.  This means that the structure:
>> >>>
>> >>>>----%tassel
>> >>>>-------<staminate floret; synonym: male floret
>> >>>>----------<androecium
>> >>>>-------------<stamen
>> >>>>----------------<anther
>> >>>>----------------<stamen filament
>> >>>
>> >>>also should include gynoecium, pistil (and nucellus, ultimately), and
>> >>>ovary, but not style and stigma.   As long as style and stigma are
>> >>>daughters of pistil, there's a problem.  The gene tasselseed2 is
>>expressed
>> >>>in the young ovary of the staminate florets in the tassel, and we can't
>> >>>describe its expression pattern accurately unless staminate flowers are
>> >>>allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
>> >>>gynoecium" certainly seems like a step in the right direction, as
>>long as a
>> >>>search on gynoecium will find the rudimentary ones as well.
>> >>>toby
>> >>>
>> >>>
>> >>>>Lincoln Stein wrote:
>> >>>>
>> >>>>
>> >>>>>The stigma issue is harder and I suspect it represents an incorrect
>> >>>>>structure
>> >>>>>in the tassel->floret->gynoecium->pistil path.
>> >>>>>
>> >>>>
>> >>>>The problem with maize is often the male and female florets occur in the
>> >>>>female
>> >>>>and male inflorescences respectively. Though this is not a normal
>> >>>>condition. I
>> >>>>agree with Sue, when we have the implementation of slots/properties
>>linking
>> >>>>different anatomical terms at some point in future, we should be able to
>> >>>>build
>> >>>>the correct structures. Please let me know if the following structure
>> >>>
>> >>>works.
>> >>>
>> >>>>inflorescence
>> >>>>----%tassel
>> >>>>-------<staminate floret; synonym: male floret
>> >>>>----------<androecium
>> >>>>-------------<stamen
>> >>>>----------------<anther
>> >>>>----------------<stamen filament
>> >>>>----%spike
>> >>>>------%spike  (sensu zea); synonym:cob
>> >>>>-------<pistillate floret; synonym: female floret
>> >>>>----------<gynoecium
>> >>>>-------------<pistil
>> >>>>---------------<style
>> >>>>---------------<stigma
>> >>>>---------------<ovary
>> >>>>----%panicle
>> >>>>--------<perfect floret
>> >>>>----------<gynoecium
>> >>>>------------<pistil
>> >>>>--------------<style
>> >>>>--------------<stigma
>> >>>>--------------<ovary
>> >>>>----------<androecium
>> >>>>------------<stamen
>> >>>>--------------<anther
>> >>>>--------------<stamen filament
>> >>>>----%capitulum (sensu compositae)
>> >>>>--------<ray floret
>> >>>>--------<disc floret
>> >>>>----<floret
>> >>>>------%floret
>> >>>>--------%ray floret
>> >>>>--------%disc floret
>> >>>>------%floret (sensu Poaceae)
>> >>>>--------%perfect floret
>> >>>>----------<gynoecium
>> >>>>------------<pistil
>> >>>>--------------<style
>> >>>>--------------<stigma
>> >>>>--------------<ovary
>> >>>>----------<androecium
>> >>>>------------<stamen
>> >>>>--------------<anther
>> >>>>--------------<stamen filament
>> >>>>--------%imperfect floret
>> >>>>----------%staminate floret; synonym: male floret
>> >>>>-------------<androecium
>> >>>>---------------<stamen
>> >>>>---------------<anther
>> >>>>----------%pistillate floret; synonym: female floret
>> >>>>-------------<gynoecium
>> >>>>----------------<pistil
>> >>>>------------------<style
>> >>>>------------------<stigma
>> >>>>------------------<ovary
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>>Lincoln
>> >>>>>
>> >>>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>> >>>>>
>> >>>>>
>> >>>>>>Hi all -
>> >>>>>> Felipe has made great progress here downloading the various programs
>> >>>>>>necessary for viewing and manipulating the ontologies.  He's run into
>> >>>
>> >>>some
>> >>>
>> >>>>>>mechanical problems that he can sort out with Pankaj, the most
>>critical
>> >>>>>>being trying to get two DagEdit windows open at the same time so two
>> >>>>>>ontologies can be viewed side by side.  In terms of the ontologies
>> >>>>>>themselves, we immediately found a number of terms that are not in
>>common
>> >>>>>>use, or are in odd hierarchical relationships; these should be easy
>> >>>
>> >>>enough
>> >>>
>> >>>>>>to change.
>> >>>>>> A more interesting and complex issue comes with species-specific
>>terms.
>> >>>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>> >>>>>>"fruit" if one is working with multiple species.  A more difficult
>>one is
>> >>>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>> >>>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>> >>>>>>tassels, because the gynoecium stops developing.  Similarly,
>>"abscission
>> >>>>>>zone" is part of "silique" in Arabidopsis, and would end up being
>>part of
>> >>>>>>"fruit" if "silique" were interpreted as an instance of "fruit".
>> >>>
>> >>>However,
>> >>>
>> >>>>>>abscission zones do not form in the grass fruit so couldn't be a
>>part of
>> >>>>>>fruit.  in both cases we end up violating the True Path Rule.  It
>>may be
>> >>>>>>that this is inevitable, since the descriptors aren't strictly
>> >>>>>>hierarchical.   Obviously one can get around this somewhat by creating
>> >>>>>>species-specific bits of the hierarchy, and by making creative use of
>> >>>>>>"sensu"; this will probably work fine as long as the ontology only
>>has to
>> >>>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to
>>make it
>> >>>>>>apply to all flowering plants, though, there may be a limit to how
>> >>>>>>species-specific we make the ontologies.   For example we could divide
>> >>>>>>fruits into indehiscent and dehiscent and then have abscission zone
>> >>>
>> >>>as part
>> >>>
>> >>>>>>of dehiscent fruits, which would be OK until we get to a fruit
>>that forms
>> >>>>>>an abscission zone but doesn't dehisce.  Another possibility that
>>Felipe
>> >>>>>>and I explored a little would be to add another category of
>>connection,
>> >>>>>>such as "a process that can occur in"  - in addition to "is part
>>of", "is
>> >>>>>>an instance of" and "develops from".  I suspect that another category
>> >>>
>> >>>might
>> >>>
>> >>>>>>create more problems than it solves, but it seemed worth considering.
>> >>>>>> Any thoughts on this are welcome!
>> >>>>>>Toby
>> >>>>>>
>> >>>>>>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/
>> >>>>>
>> >>>>>
>> >>>>--
>> >>>>******************************************
>> >>>>Pankaj Jaiswal, Ph.D.
>> >>>>Research Associate
>> >>>>Dept. of Plant Breeding
>> >>>>Cornell University
>> >>>>Ithaca, NY-14853, USA
>> >>>>
>> >>>>Tel:+1-607-255-3103 / Fax:+1-607-255-6683
>> >>>>E mail: pj37 at cornell.edu
>> >>>>http://www.gramene.org
>> >>>>******************************************
>> >>>
>> >>>
>> >>>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/
>> >>>
>> >>>
>> >>>
>> >>
>>
>>>>------------------------------------------------------------------------------
>>-
>> >>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>> >>The Arabidopsis Information Resource	FAX: (650) 325-6857
>> >>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>> >>Department of Plant Biology		URL: http://arabidopsis.org/
>> >>260 Panama St.
>> >>Stanford, CA 94305
>>
>>>>------------------------------------------------------------------------------
>>-
>> >
>> >
>> >
>> > 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/
>> >
>> >
>> >
>>
>> --
>> ******************************************
>> Pankaj Jaiswal, Ph.D.
>> Research Associate
>> Dept. of Plant Breeding
>> Cornell University
>> Ithaca, NY-14853, USA
>>
>> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
>> E mail: pj37 at cornell.edu
>> http://www.gramene.org
>> ******************************************
>>
>>
>>
>
>-------------------------------------------------------------------------------
>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>The Arabidopsis Information Resource	FAX: (650) 325-6857
>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>Department of Plant Biology		URL: http://arabidopsis.org/
>260 Panama St.
>Stanford, CA 94305
>-------------------------------------------------------------------------------


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/

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