POC observations so far

[Sue Rhee]

Toby,

Great items for discussion. I agree that invoking another category will
make things more complex than desirable, at least in the beginning. Also,
the category you want to bring in (process that can occur in) can be a
good example of composite ontology use in the future (anatomy + process
ontologies).

I have to think about the stigma example more but regarding the abscission
zone, I believe there should be a generic abscission zone that should a
parent of silique abscission zone, pedicel abscission zone, and petiole
abscission zone. These children can then be children of silique, pedicel,
and petiole, respectively. Otherwise, we are going to violate true path
rule as soon as we have a gene that is specifically expressed in the
petiole abscission zone.

I totally agree that 'sensu' solution is something to be considered as a
last resort. Nonetheless, I think we should try to be economical in
brining in generic parental terms, in order to minimize complexity and
possibly to prevent getting into more sticky situation later. So I'm not
sure about the need to invoke indehiscent and dehiscent fruits. If we did
this, how many parts of fruits will have to be separated to go into
different branches of the fruit?

Sue

>   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/
>
>
>

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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.
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