[Ontology-editors] another question about biogenesis/organization

[Valerie Wood]

Others may be happy to have these terms to be in independent branches. I 
think though, that intuitively a biologist would expect to be able to 
retrieve both of these cell wall associated processes with a single 
term. I'm sure that most people don't even realise that they can't..... 
It took me a while to realise that this was the case when some gene 
products with only a "cell wall biogenesis" annotation weren't being 
slimmed.


Valerie Wood wrote:

> "organization and biogenesis" ? ;)
>
>
> Midori Harris wrote:
>
>> Ow, my head.
>>
>> I think we've worked out reasonable definitions for "organization" 
>> and "biogenesis" and we're just about there for applying them 
>> consistently. What we don't have -- and apparently you could really 
>> use -- is some term that covers everything we're putting under both 
>> organization and biogenesis ... "anything that happens to a cellular 
>> component".
>>
>> What to call it, though?
>>
>> m
>>
>> On Tue, 16 Jun 2009, Valerie Wood wrote:
>>
>>>
>>>
>>> Sorry, I still haven't got my head around this...see my recent SF 
>>> item.....problem with my slimming
>>> I am still trying to get a slim for a tutorial which gives good 
>>> coverage of all of my annotated gene products.
>>>
>>> Previously I had the term "cell wall organization and biogenesis" 
>>> which covered all of cell wall organization and biogenesis.
>>>
>>> Now organization and biogenesis are "disjoint" (am I using the 
>>> correct terminology?) I need to include *Both* the organization and 
>>> biogenesis term, when it seems as though I really want one term to 
>>> cover both of these cell wall processes at this level, and that they 
>>> are intimately related. I'm not sure how my original annotations got 
>>> split between the the 2 new terms but there isn't much overlap 
>>> now......
>>>
>>> 73 to biogenesis
>>> and 63 to organization
>>> 21 to both
>>> However when I look through the list I am pretty sure all of those 
>>> annotated to biogenesis to equally be annotated to organization.
>>>
>>> Now, if i don't include both of these terms in the slim, I get gene 
>>> products which do not map to a high level term.
>>>
>>> Any thoughts?
>>>
>>> Val
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.