POC observations so far

Sun Oct 5 20:47:12 EDT 2003

Yes- TAIR has made some use of derived from though not as comprehensively
as we could (e.g. trichome is derived from meristemoid, root hair derived
from trichoblast).But not say- leaf derived from leaf primordia.
Leonore

On Sat, 4 Oct 2003, Lincoln Stein wrote:

> 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)
>

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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
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