POC observations so far

Fri Oct 3 14:52:01 EDT 2003

 >>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
******************************************