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

[Valerie Wood]

Sorry for the delay.
Are there any examples of biogenesis which cause TVPs (I can see why 
assembly would but not biogenesis)
Val


Midori Harris wrote:

> 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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>



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