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

[Midori Harris]

For the amine/amino/etc. terms, I wonder if the best fit between ChEBI and
GO might be:

   GO:amine_metabolism =def GO:metabolism that has_participant
ChEBI:organic_amino_compound

... even though the names don't quite match (we can edit the GO name and 
def). At a quick glance, the children of the ChEBI term cover everything 
currently grouped under amine metabolism in GO, and I didn't spot any 
children in GO that obviously wouldn't work with this.

Has_part is apparently used in ChEBI, although I don't come across it 
often. It's on their list of relationship types, with an example linked.

m

On Fri, 26 Jun 2009, Jane Lomax wrote:

> 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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>
>
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