POC observations so far

Fri Oct 3 13:26:52 EDT 2003

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/