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

[Midori Harris]

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.

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