[Ontology-editors] small molecule metabolism

[Valerie Wood]

Of course if this is just not feasible without being contrived we should 
forget it.

I did have an which might work although it perhaps sounds  a bit odd
"metabolite metabolic process"
or "metabolome metabolic process"
would fit.
http://en.wikipedia.org/wiki/Metabolite


 






Tanya Berardini wrote:

>
>
> On Thu, Apr 9, 2009 at 8:48 AM, Chris Mungall <cjm at berkeleybop.org 
> <mailto:cjm at berkeleybop.org>> wrote:
>
>
>     On Apr 9, 2009, at 3:35 AM, Valerie Wood wrote:
>
>         It seems like there is a gap in the terminology of biology to
>         decribe "everything that is not a macromolecule molecule".
>         Maybe we should make one up....
>         Perhaps "small molecule metabolism" would be acceptable if it
>         is defined as "everything that is not a macromolucule" but
>         that is not an acceptable way of defining something is it?
>
>
>     Do we really need a term for it? Why not just ask for non-X
>     metabolism any time you're interested in metabolism of Ys where Ys
>     are not Xs
>
>     Granted tools can't do this yet but it's not hard given the
>     correct structures in the ontology, and we should perhaps be
>     working towards a situation where tools do support this
>
>
> I am partial to this approach.  Defining 'small molecule metabolism' 
> as everything that is not 'macromolecule metabolism' violates the 
> ontology design principle of positivity.  Why not just combine the 
> annotations from the terms that do cover what is desired and then 
> analyze those results?
>
> Tanya
>



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