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

[Midori Harris]

All righty then, I'll barely scratch the surface this week, but I'll fix 
what I've spotted so far.

m

On Tue, 30 Jun 2009, Chris Mungall wrote:

>
> Go for it. The only reason to hold off would be the magnitude of the task of 
> getting all the bp_xp_chebi logical definitions complete. But it's a good 
> idea to fix ones that are obviously wrong as you go along
>
> On Jun 30, 2009, at 7:07 AM, Midori Harris wrote:
>
>> 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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>