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

[Chris Mungall]

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