POC observations so far

[Lincoln Stein]

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/

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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