[Ontology-editors] organization, biogenesis etc

[Midori Harris]

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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