[Ontology-editors] small molecule metabolism

[Tanya Berardini]

On Thu, Apr 9, 2009 at 8:48 AM, Chris Mungall <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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