POC observations so far

[Leonore Reiser]

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/
>
>
>

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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
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