[Ontology-editors] small molecule metabolism

[Valerie Wood]

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?

I looked through the lists briefly and I didn't spot any anomalies....

Val


Chris Mungall wrote:

>
> On Apr 8, 2009, at 6:29 AM, Midori Harris wrote:
>
>> Hi,
>>
>> Val has asked about adding a term to group small molecule metabolism  
>> separately from macromolecule metabolism. The initial request came a  
>> few months ago, and has been reiterated today. We've been hung up on  
>> how such a term could be named and defined, since "small molecule"  
>> is kind of a woolly concept that is hard to map onto, say, one  
>> branch of ChEBI.
>
>
> We could try:
>
> / CHEBI:24431 ! molecular structure
>   is_a CHEBI:23367 ! molecular entity
>    is_a CHEBI:36357 ! polyatomic entity
>     is_a CHEBI:25367 ! molecule
>     is_a CHEBI:33595 ! cyclic compound
>     is_a CHEBI:33731 ! clusters
>     is_a CHEBI:33839 ! macromolecule ***
>     is_a CHEBI:36358 ! polyatomic ions
>     is_a CHEBI:37577 ! heteroatomic molecular entities
>     is_a CHEBI:46662 ! mineral
>     is_a CHEBI:50795 ! nanostructure
>     is_a CHEBI:50967 ! non-covalently-bound molecular entities
>
> one option is to simply try it with anything that is not a  
> macromolecule.
>
> Using biological_process_xp_chebi (incomplete) I find 143 subtypes of  
> metabolism that have some kind of macromolecule as a participant  
> (participant defined very generally as in the sense of the RO), and  
> 2136 that only have non-macromolecules as participants.
>
> This is an overestimate for a number of reasons: 219 of these refer 
> to  CHEBI terms that are is_a-incomplete. Of the remainder, there may 
> be  some that have unusual classification in CHEBI. E.g.
>
>  / CHEBI:24431 ! molecular structure
>   is_a CHEBI:23367 ! molecular entity
>    is_a CHEBI:33579 ! main group molecular entity
>     is_a CHEBI:33675 ! p-block molecular entities
>      is_a CHEBI:33582 ! carbon group molecular entities
>       is_a CHEBI:50860 ! organic molecular entity
>        is_a CHEBI:33243 ! natural product
>         is_a CHEBI:23008 ! carbohydrate ***
>
> I'm attaching the lists. I think it may be a useful exercise to  
> investigate the false +ves and report back to CHEBI
>
>
>>
>> Does anyone have any clever ideas for the ontology? Or are there  
>> tools that could help with Val's genome-wide analysis using the  
>> existing GO graph?
>>
>> https://sourceforge.net/tracker/index.php?func=detail&aid=2106200&group_id=36855&atid=440764 
>>
>>
>> Thanks,
>> midori
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>>
>



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