[Ontology-editors] organization, biogenesis etc

[Jane Lomax]

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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>>>>> Ontology-editors at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>> 
>>>> 
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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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