[Ontology-editors] small molecule metabolism

[Chris Mungall]

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

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>
> 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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