POC observations so far

Sat Oct 4 15:58:33 EDT 2003

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