POC observations so far

Fri Oct 3 11:56:09 EDT 2003

Felipe Zapata wrote:
> The structure that Pankaj suggests could work, however what happens when you 
> querry the ontology? Let's say for example you querry for gynoecium.  You won't 
> retrieve Tassel at all, even though there's a "gynoecium" (incomplet, imperfect) 
> in tassels that simply stops developing.

I think as of this time we should consider making very explicit relationships. I 
don't know if its true or not, please correct me here, will anybody search for 
gynoecium in Tassel floret. I presume not. Incase they do then alternative would 
be to have "rudimentary gynoecium", but i have no clues if it has developed 
enough to have a proper pistil.

-%gynoecium
---%rudimentary gynoecium
---<pistil
------<stigma
------<style
------<ovary

----%tassel
-------<staminate floret; synonym: male floret
----------<androecium
-------------<stamen
----------------<anther
----------------<stamen filament
----------<rudimentary gynoecium

> 
> Felipe
> 
> 
> Quoting Pankaj Jaiswal <pj37 at cornell.edu>:
> 
> 
>>
>>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
>>******************************************
>>
>>
>>
> 
> 
> 
> _____________
> Felipe Zapata
> University of Missouri-St.Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis MO, 63121
> Phone: (314) 516-6200
> Fax: (314) 516-6233
> 

-- 
******************************************
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
******************************************