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

[Chris Mungall]

On Jul 6, 2009, at 9:50 AM, Midori Harris wrote:

> I've now gone through the newlinks file and added a lot of the  
> suggested links. There were some (~100) that I wasn't sure about, so  
> have not added for the moment. Many of the questionable ones refer  
> to nucleosides or nucleotides -- I wonder if some of ChEBI's is_a  
> links would be better as has_part (e.g. nucleotides has an is_a path  
> to carbohydrate)?

I think these results are very useful and should be added to the CHEBI  
tracker.

> I've also made a few improvements to the xps themselves based on my  
> evaluation of the newlinks.

Great, thanks

This got rid of 1144 misalignments... but revealed 1058 new ones!

> It might be worth generating updated versions of the newlinks and  
> mismatch files.

done.

> I did try to load up the imports file, but OBO-Edit squawked about  
> unrecognized relations.

currently fixing the set of relations used

>
> midori
>
> On Tue, 30 Jun 2009, Midori Harris wrote:
>
>> 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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