POC observations so far

Sat Oct 4 13:46:30 EDT 2003

We should also consider whether it will help to add more relationship types, 
such as "derived from".  It does not seem to me to be appropriate to describe 
a temporal development relationship between two organs as either "isa" or 
"partof"

Lincoln

On Friday 03 October 2003 01:26 pm, 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/

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)