POC observations so far

[Leonore Reiser]

My recollection with GO is that part if is CAN be a part of but not IS
always a part of.
Can the flower problem be resolved with perfect/imperfect/female/male??or
more appropriate morphological terms?


On Fri, 3 Oct 2003, Lincoln Stein wrote:

> Hi,
>
> I'm not sure that the abscission zone problem represent a violation of the
> true path rule.  In the sequence ontology, we have introns being parts of
> primary transcripts, and it doesn't seem to matter that prokaryotes'
> transcripts don't have introns.  Some species will simply not have a
> particular part.
>
> The stigma issue is harder and I suspect it represents an incorrect structure
> in the tassel->floret->gynoecium->pistil path.
>
> 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/
>
> --
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>
>
>

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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/
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