[Ontology-editors] organization, biogenesis etc

[David Hill]

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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>>
>