[Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI

[Jane Lomax]

Hi Chris - I guess I thought that in the situation like the 
glutamine/amine one you describe we would actually change our classes to 
reflect ChEBI - i.e. we would obsolete (or merge/rename) 'cellular amine 
metabolism' rather than trying to model what we already had in a rather 
awkward way. So we might have:

carboxylic acid metabolism
---[i] amino acid metabolism
------[i] glutamine metabolism

or whatever classes we chose from ChEBI - a ChEBI slim might be useful 
here actually.

Not sure what we do about multiple is_a inheritance in ChEBI though. 
Maybe it would be possible to use a single-inheritance slim?

Jane





Chris Mungall wrote:
> Ideally we could reconstitute many of the existing asserted links in  
> GO from CHEBI, and ultimately rely entirely on CHEBI. At the moment  
> we're missing some relationships to do this.
>
> For example, currently we have:
>
> GO:glutamine_metabolism =def GO:metabolism that has_participant  
> CHEBI:glutamine
> GO:cellular_amine_metabolism =def GO:metabolism that has_participant  
> CHEBI:amine
>
> GO also asserts that glutamine_metabolism is_a  
> cellular_amine_metabolism. We should in principle be able to remove  
> this link and re-infer it from the logical definitions and the  
> relationships in CHEBI. This doesn't work, because glutamine is not a  
> subclass of amine in CHEBI.
>
> We can probably do a little better than the logical definitions above
>
> * We should use CHEBI:L-glutamine rather than glutamine
> * We can have a logical definition of cellular amine metabolic process  
> that better reflects the text definition:
>
> GO:0009308 ! cellular amine metabolic process ***  [DEF: "The chemical  
> reactions and pathways involving any organic compound that is weakly  
> basic in character and contains an amino or a substituted amino group,  
> as carried out by individual cells. Amines are called primary,  
> secondary, or tertiary according to whether one, two, or three carbon  
> atoms are attached to the nitrogen atom."]
>
> Taking the text definition literrally suggests that CHEBI:amino_group  
> is the class to use. We could assign a logical definition to  
> cellular_amine_metabolism
> 	GO:metabolism that has_participant (anything that has_part  
> CHEBI:amino_group)
>
> Or we can simply use:
> 	GO:metabolism that has_participant CHEBI:amino_group
>
> With has_participant being transitive over has_part
>
> However, this is still insufficient to recapitulate the asserted  
> relationship in GO, because there is nothing in CHEBI that tells me  
> that L-glutamine (or any amino acid) has_part (or any other  
> relationship to) amine or amino group.
>
> I think in this case we need a has_part relationship added to CHEBI,  
> we can then recapitulate the relationship in GO.
>
> This is just one single example though. There are plenty of others,  
> some will be less straightforward. See for example:
> http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi#Misalignments_and_reasoner_results
>
>
> 	
>
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
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