POC observations so far

[Pankaj Jaiswal]

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
******************************************