[Ontology-editors] organization, biogenesis etc

[Chris Mungall]

For the capsule case too?

On Oct 4, 2008, at 11:18 AM, David Hill wrote:

> 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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