[Ontology-editors] organization, biogenesis etc

[Karen Christie]

but I'm not sure there's anything different about actin assembly in 
'maintenance' versus 'biogenesis', so it seems kind of artificial to 
separate it.

-Karen


On Mon, 27 Oct 2008, David Hill wrote:

> No, but then it would be involved in assembly.
>
> Karen Christie wrote:
>> 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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