[Ontology-editors] organization, biogenesis etc

[David Hill]

I agree the relationship should be part_of.

David

Midori Harris wrote:
> Hi Chris,
>
> We plan to make a distinction between "organization" and "biogenesis" 
> such that biogenesis includes synthesis of components and organization 
> doesn't. So ...
>
> organization and biogenesis -> organization
> and
> biogenesis - > biogenesis (but with a clearer definition)
>
> Good that you've spotted the inconsistencies in those wall and capsule 
> terms. We should clean it up into
>
> biogenesis
> - [p] organization
> - [p] part biosynthesis
>
> e.g.
>
> GO:0009272 ! fungal-type cell wall biogenesis
> - part_of GO:0031505 ! fungal-type cell wall organization
> -- part_of GO:0051278 ! fungal-type cell wall polysaccharide 
> biosynthetic process
>
> m
>
> On Fri, 3 Oct 2008, Chris Mungall wrote:
>
>>
>> Sometimes the biosynthesis of constituent molecules is a kind of 
>> organization of the component:
>>
>>      is_a GO:0045230 ! capsule organization
>>        is_a GO:0045227 ! capsule polysaccharide biosynthetic process ***
>>
>> Sometimes it is part_of:
>>
>>        is_a GO:0031505 ! fungal-type cell wall organization
>>         is_a GO:0009272 ! fungal-type cell wall biogenesis
>>          pt_o GO:0051278 ! fungal-type cell wall polysaccharide 
>> biosynthetic process ***
>>
>> Let me know which it is, and we will encode it in the relation -- 
>> then the reasoner can fix these in one fell swoop...
>>
>> On Oct 3, 2008, at 11:46 AM, Chris Mungall wrote:
>>
>>> From the latest meetings summarized here:
>>> http://wiki.geneontology.org/index.php/Cellular_component_processes
>>>
>>> X organization and biogenesis -> X organization
>>> X biogenesis -> X organization
>>>
>>> (with synonyms retained, exceptions allowed etc)
>>>
>>> This is great - I was never quite sure how to write the XP 
>>> definitions for these terms before, which resulted in the reasoner 
>>> giving curious results. I had to filter them before submitting 
>>> tracker items.
>>>
>>> Now these terms will make use of a single relation in all their XP 
>>> definitions, results_in_organization_of
>>>
>>> I can go ahead and add these today then run the reasoner (I think 
>>> there will be a lot of graph changes suggested..). Even though the 
>>> renaming is not complete, I will go ahead on the assumption that the 
>>> two changes above are being made.
>>>
>>> Note that if I do this the reasoner will infer equivalence between 
>>> "cell projection biogenesis" and ""cell projection organization and 
>>> biogenesis". This seems fine, since from my reading of the above 
>>> page these will be merged anyway.
>>>
>>>
>>>
>>>
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>>
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