[Ontology-editors] question about cellular component organization (from bp-xp-cc evaluation)

[Chris Mungall]

On Jun 16, 2009, at 9:11 AM, Midori Harris wrote:

> Hi,
>
> So I finally overcame my fear of OBO-Edit making mincemeat of  
> unrecognized relations, and  loaded the bp-xp-cc imports into OE for  
> the first time in months.

Hmm. If you load from the imports file then every relation used in  
bp_xp_cc should be declared. Some still lack text definitions.

> The very first implied link in the list (upon Edit -> Assert implied  
> links) raises a question:
>
>  Assert: protein complex assembly is_a cellular macromolecular  
> complex assembly
>
> I found the explanation a bit bewildering, but I think I see where  
> the implication is coming from.

Yes, the display of the 'explanations' is not very good. OE 2.1 will  
allow you to click on the inferred link and then look at it in the  
view of your choice. In most cases this will be superior to attempting  
to follow the logical proof.


> We've deliberately created separate terms for protein complex  
> assembly and cellular protein complex assembly (with parallel  
> structures for macromolecular complex assembly and m. c. subunit  
> organization) because some complexes are assembled at the  
> multicellular-organism level. The circulating lipoprotein complexes  
> -- HDL, LDL, etc. -- are examples.
>
> So it seems that, instead of asserting the implied link, we actually  
> have to move cellular component organization and cellular component  
> biogenesis directly under biological process, not under cellular  
> process. This will fix a bunch of other implied links too, I think.
>
> I've also put this on the wiki:
> http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component#2009-06-16
>
> Comments welcome!

So the inferences here follow from definitions that use the has_level  
relation. For example, cellular process = biological_process that  
has_level cell.

I'm really not sure the best way of defining has_level. But it seems  
that if we use this relation in logical definitions for terms that say  
"cellular <BP>" then the reasoner can at least make us consistent, as  
it has in the case above.

>
> cheers,
> m
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