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

[Chris Mungall]

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
>>
>>
>> 	_______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>