[Ontology-editors] organization, biogenesis etc

[Karen Christie]

I'm not complete sure that assembly of actin filaments is always 
maintenance. Are they sometimes completely disassembed and then completely 
assembled from scratch? If so, that wouldn't be maintenance.

-Karen


On Fri, 24 Oct 2008, David Hill wrote:

> I think this is certainly better as well. I think perhaps we should have 2 
> children of 'assembly', 'assembly involved in biogenesis' and 'assembly 
> involved in  maintenance'. I think that the actin process would be the 
> latter.
>
> david
>
> Jane Lomax wrote:
>> Yep, that's definitely better. The only thing that worries me is the 
>> placement of assembly under biogenesis - for something like an actin 
>> filament that is disassembled and then reassembled continuously, would that 
>> be right? i.e. would it be right to call that sort of reassembly 
>> 'biogenesis'?
>> 
>> jane
>> 
>> 
>> On Tue, 21 Oct 2008, Midori Harris wrote:
>> 
>>> 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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