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

[Midori Harris]

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've also made a few improvements to the xps themselves based on my 
evaluation of the newlinks. It might be worth generating updated versions 
of the newlinks and mismatch files.

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

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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