[Ontology-editors] another question about biogenesis/organization

[Jane Lomax]

Being able to have union terms in GO slims would solve this. I'm not 
sure it's something we would want to code into the ontology.

Can map2slim handle term unions, Chris?

Jane

Midori Harris wrote:
> Seriously, the problem with "and" is that it could make a gene product 
> annotated to a descendant term look like it's involved in everything 
> covered by a parent (e.g. annotate to biogenesis and imply annotation 
> also to organization, which includes disassembly).
>
> so that doesn't rule out "organization or biogenesis" ...
>
> m
>
> On Wed, 17 Jun 2009, 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>>
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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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