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

[Chris Mungall]

On Jun 26, 2009, at 5:15 AM, Midori Harris wrote:

> 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.

OK, that looks like it will work nicely.

I'm not sure which of the is_a parents of amino acid in CHEBI would be  
primary, organic amino compound or carboxylic acid.

> 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.

There are 715 uses in the latest release. I suspect we'll be seeing  
more of them

>
> 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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>>
>>
>>
>