[Ontology-editors] small molecule metabolism

[Chris Mungall]

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

Do you view cabrohydrate as a macromolecule? Either CHEBI or Wikipedia  
should be modified here

>
> 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
>>> _______________________________________________
>>> Ontology-editors mailing list
>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>
>>
>
>
>
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