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

[Midori Harris]

Any assembly term that causes a TPV will also cause a biogenesis TPV, 
because assembly is part_of biogenesis.

m

On Mon, 29 Jun 2009, Valerie Wood wrote:

> 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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