POC observations so far

[Sue Rhee]

Sounds good. There are currently four nodes where this relationship
resides in the Arabidopsis anatomy ontologies.

parent nodes:
+-------------+
| name        |
+-------------+
| trichoblast |
| silique     |
| ovary wall  |
| L1          |
+-------------+

Sue


On Sat, 4 Oct 2003, Felipe Zapata wrote:

> Actually that relationship already exists. At least TAIR uses:
>
> !version: $Revision: 1.13 $
> !type: % ISA Is a
> !type: < PARTOF Part of
> !type: ~ DEVELOPSFROM develops from
> !editors: Leonore Reiser, Jonathan Clarke
> $Arabidopsis ontology ; TAIR:0000001
> .....
> ..
> ..
>
> What we probably need to do, is to go through the current ontologies and look for
> nodes where this relationship would have more biological meaning.
>
> Felipe
>
>
> Quoting Lincoln Stein <lstein at cshl.edu>:
>
> > 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)
> >
>
>
> _____________
> 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
>

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------