progress and thought questions

[Toby Kellogg]

Thanks Pankaj -
  Just a couple of quick responses while I am thinking of it:
>
>> 7.  Is it worth including perigynium as an instance of a prophyll?  The
>> term is used only for species in the family Cyperaceae, specifically
>> species of Carex.
>
>My argument would be to include the terms on usage/requirement basis
>unless absolutely necessary to clarify some other node in the ontology.

this sounds like a good principle to me.

>
>> 10.  Inflorescence can be defined with panicle, raceme, tassel, ear, and
>> cob as synonyms.  Alternatively, we can divide inflorescences into racemes
>> (which do not terminate in a flower) and cymes (which do).  Panicle,
>> tassel, ear, and cob would thus be synonyms of raceme.  Or we can keep
>> dividing the inflorescence categories more and more finely depending on
>> which axes end in flowers and which don't, and could end up with a
>> plethora
>> of terms.  (Same issue as #s 2, 4, and 8.)  How complex do we get?
>
>I agree with you. My question here is how do we deal with terms like
>primary/secondary inflorescence branches? There are many mutants/genes
>responsible for the branching organization.

This gets back to the goal of the ontology.  For the many mutants/genes
that affect inflorescence branching, do we need to be able to describe each
of them in detail (in which case we need lots of terms) or just to assign
them to the bin "inflorescence" (in which case we only need a few terms)?
I don't know the answer to this, but it will affect the structure I think.
i.e., will we want to make queries such as "find all genes in any plant
that, when mutated, affect phyllotaxis on third order inflorescence
branches", or will it be sufficient to ask "what genes are expressed in
inflorescences"?
  Food for thought anyway.
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/