[Ontology-editors] organization, biogenesis etc

[Jane Lomax]

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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>> 
>> 
>

-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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