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

Tue Jul 7 03:57:36 PDT 2009

Hi Midori,

Midori Harris wrote:
> On Mon, 6 Jul 2009, Chris Mungall wrote:
>
>   
>>> 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.
>>     
>
> OK. ChEBI people - is there a tracker (Trac, SourceForge, or similar), or 
> should I just email? Or register as a submitter? Let me know how you want 
> to get the feedback.
>
> I'm also putting a summary of what I've done, and outstanding questions, 
> on the GO SF tracker item.
>   
Can we get back to you on this one. We were intending to look at these 
at our group meeting tomorrow. We'll then get back and let you know the 
best way to proceed.
Its most likely going to be the SF tracker as the Submission tool does 
not allow updates yet.

Cheers,
P
>   
>>> 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!
>>     
>
> I haven't tackled the misalignments directly yet, but will take a look 
> (after a pause to deal with some recent GO SF items). I'll also look at 
> the updated newlink file.
>
>   
>>> 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
>>     
>
> Thanks!
>
> m
>
>   
>>> 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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>>>>>>>               
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>>>>         
>
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-- 
Paula de Matos
<pmatos at ebi.ac.uk>
ChEBI & IntEnz Coordinator 
European Bioinformatics Institute - EMBL