[Ontology-editors] another question about biogenesis/organization

[Valerie Wood]

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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>
>



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