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

[Midori Harris]

Hi all,

Has anyone had any further thoughts or flashes of insight? If not, I think 
I ought to go ahead with moving CC organization and CC biogenesis to 
remove the TPV. For the time being, I'll just add cellular process 
parentage back to the children of CC org and CC biogen that are cellular; 
the option of creating parent terms to collect them would remain open, 
should we ever come up with term names that aren't hideous.

If there are no objections I'll do the deed at the end of this week.

midori

On Wed, 17 Jun 2009, Midori Harris wrote:

> A bit of further thinking below ...
>
>>> 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.
>
> What rang the alarm bells is that the reasoner was suggesting links to a 
> "cellular" parent for terms that are not themselves "cellular <bp>", like the 
> example I included:
>
>> Assert: protein complex assembly is_a cellular macromolecular complex 
> assembly
>
> Obviously we ought to fix the inconsistency that's spawning those finds, 
> rather than add the links as suggested. The 
> biological_process_xp_cellular_component.obo file doesn't actually have any 
> xps for "cellular component organization" or "cellular component biogenesis"; 
> I think the problem is that both are is_a "cellular process".
>
> But if we just move "cellular component organization" and "cellular component 
> biogenesis" up to be direct is_a children of "biological process", some of 
> the descendants will lose paths to "cellular process". The simplest solution 
> is just to add the "cellular process" parent back to terms such as "cellular 
> macromolecular complex subunit organization". A lot of fairly specific terms 
> would end up directly under "cellular process" this way (e.g. "cytoplasm 
> organization", "synaptogenesis"). Maybe we can live with that, although it 
> would be neater to have "cellular <BP>" terms to group them. The catch with 
> the better-organized approach is names for some of the terms -- "cellular 
> cellular component assembly" sounds absolutely ridiculous, and words can't 
> express how confused our users would be.
>
> Any thoughts?
>
> m
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