POC observations so far

Fri Oct 3 14:58:26 EDT 2003

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
-------------------------------------------------------------------------------