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

[Midori Harris]

Hi all,

Now I'm taking a closer look at the 
biological_process_xp_chebi-newlinks.txt, and there are a bunch of dodgy 
link suggestions that I think trace to xps that don't use the best 
available ChEBI differentia(e). Is there any reason not to change the xps 
in biological_process_xp_chebi.obo when I spot ones that can be improved?

m

On Thu, 25 Jun 2009, 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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