[Ontology-editors] another question about biogenesis/organization

[Jane Lomax]

Yeah, I know what you mean Val. I'm sure we often use union terms 
because there is no neat name to encompass the meaning of the two terms. 
They do cause problems for building the ontology though.

Don't think 'cell physiology' would work - we got rid of all the 
physiology terms because we couldn't define them as distinct it from the 
metabolism terms...

Jane

Valerie Wood wrote:
> This sounds quite complicated (for users), but it would be useful if 
> there is no way to create the "compound terms" . It seems though, that 
> these are often reasonable biological concepts but we don't have a 
> good way to name them with a grouping term (there must be something 
> which covers both organization and biogenesis....)
>
> It is similar to the situation with "small molecule metabolism"
> http://sourceforge.net/tracker/?func=detail&aid=2106200&group_id=36855&atid=440764 
>
>
> val
>
> Chris Mungall wrote:
>
>>
>> Currently, no.
>>
>> But we are reengineering a lot of the software. The new framework  
>> allows for arbitrary boolean intersection/union combinations. We  
>> should have this in a standalone script soon, but maybe a bit longer  
>> for amigo
>>
>> (we're already using taxon unions for the GAF validation checks)
>>
>> On Jun 17, 2009, at 5:03 AM, Jane Lomax wrote:
>>
>>> 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
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>>
>>> _______________________________________________
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>>>
>>
>>
>
>
>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468