[Ontology-editors] small molecule metabolism

[Valerie Wood]

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
>

Its quite difficult  to do this during enrichment analysis.
I have seen  a number of times that   terms which would be classically 
termed "biochemical pathways" are enriched, bacause I see the 
annotations  in my data individually.
The enrichment tools don't show this  because the number of annotations 
to the individual  terms are not large enough. tThe parent term 
"cellular metabolic process" is not enriched because the effect is 
masked  by all of the other 3000 annotations to this term generated  
mainly by the variouse types of macromolecule metabolic process i.e.DNA 
metabolic process, protein metabolic process etc.

When you are analysisng whole genome datasets it isn't really practical 
to add and subtract processes and repeat enrichment (it gets way too 
complicated to process and report the results, as you would have to 
fiddle with the P-values for everything you did manually and then 
reintegrate it into your whole genome analysis)

This isn't really a problem for me now because I worked around it, but I 
could only do this because I know what the problem was.

I thought that other users may appreciate some sort of grouping term 
here for similar analyses- it just seems that there should be a term to 
group these processes in the same way that macromolecular metabolic 
processes are grouped. The fact is that if you have a bunch of genes 
enriched for low numbers of  various small metabolism/canonical 
biochemical pathway terms, this  enrichment would  most likely be 
overlooked.

val









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.