[Ontology-editors] organization, biogenesis etc

[Midori Harris]

I think what we really want is biogenesis = assembly + part synthesis, 
i.e.

organization
-[i] assembly
-[i] disassembly
-[i] maintenance
-[i] morphogensis
biogenesis
-[p] assembly
-[p] part biosynthesis

because we still (I think) want the distinction between organization and 
biogenesis to be that biogenesis includes synthesis of parts

if this looks ok I'll update the wiki

m

On Tue, 21 Oct 2008, Jane Lomax wrote:

> Yeah, this is wrong isn't it? Disassembly should not be part of biogenesis. 
> This needs a rethink...
>
> On Tue, 21 Oct 2008, Midori Harris wrote:
>
>> Looking at this again at meeting: at first I thought this would work:
>> 
>>>> biogenesis
>>>> - [p] organization
>>>> - [p] part biosynthesis
>> 
>> but we're also thinking organization has 4 children:
>> 
>> organization
>> - [i] assembly
>> - [i] disassembly
>> - [i] maintenance
>> - [i] morphogenesis
>> 
>> So I just want to make sure it still makes sense when we put it all 
>> together:
>> 
>> biogenesis
>> - [p] organization
>> --- [i] assembly
>> --- [i] disassembly
>> --- [i] maintenance
>> --- [i] morphogenesis
>> - [p] part biosynthesis
>> 
>> OK? Or do we have to make any further changes?
>> 
>> m
>> 
>> On Sat, 4 Oct 2008, 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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>
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