[Ontology-editors] organization, biogenesis etc

[David Hill]

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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