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

[Midori Harris]

Hi again,

I've had a very quick look at the newlinks.txt file.* Most of them look 
like they'll prove to be fine on closer inspection, and we'll add them 
(though it might be more convenient to wait for the new "assert implied 
links" interface in OE2).

Exceptions I've spotted so far seem to fall into two classes.

1) Cases where I suspect we've chosen a wrong ChEBI differentia; for 
example:

[ GO:0001408  !  guanine nucleotide transport ] is_a [ GO:0015854  ! 
guanine transport ]

In this case, I'm reasonably sure from the def that GO:0015854 refers to 
transport of free guanine base. We may want to change the names of some GO 
terms like GO:0001408, or at least add synonyms, and we'll certainly want 
to change some of the GO-ChEBI xps. The xp file has

[Term]
id: GO:0001408
name: guanine nucleotide transport
intersection_of: GO:0006810 ! transport
intersection_of: OBO_REL:results_in_transport_of CHEBI:16235 ! guanine

but based on the text def I think it ought to be

[Term]
id: GO:0001408
name: guanine nuceotide transport ! [could rename to "guanosine 
5'-phosphate transport"]
intersection_of: GO:0006810 ! transport
intersection_of: OBO_REL:results_in_transport_of CHEBI:37121 ! guanosine 
5'-phosphates

2)
Cases where the suggested link is backwards:

[ GO:0006829  !  zinc ion transport ] is_a [ GO:0006830  !  high-affinity 
zinc ion transport ]

Not only does "high-affinity" make GO:0006830 more specific than 
GO:0006829, we already have the link GO:0006830 is_a GO:0006829.

I'm not sure how to fix these; it seems that the child term requires an 
additional differentia not found in ChEBI or GO to capture 
"high-affinity".

2a)
In a few cases the newlinks.txt file even has a link both ways round:

[ GO:0001408  !  guanine nucleotide transport ] is_a [ GO:0015854  ! 
guanine transport ]

and

[ GO:0015854  !  guanine transport ] is_a [ GO:0001408  !  guanine 
nucleotide transport ]

We'll probably find more things as we go through the links individually.

cheers,
m

*I tried to load biological_process_xp_chebi-imports.obo into OE, but it 
calls for a file that's not in CVS, at least not in the specified 
location: go/scratch/obol-imports/chebi_lite.obo.


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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