POC observations so far

[Toby Kellogg]

Just a follow-up (messages crossing in the mail):
Unfortunately, people do search for gynoecia in tassel florets, and even
write papers about them.  (perhaps we have brain defects that make us do
these sorts of things...)  let's try the "rudimentary" solution for a while
and see how it plays out.  We'll want rudimentary stamens as well, although
that term will overlap with staminodia.
  On another subject, are we still planning a conference call on Monday?
if so, I'll have to shift the time of my lab meeting.
Toby

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


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/