[Ontology-editors] organization, biogenesis etc

[Midori Harris]

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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