[Ontology-editors] another question about biogenesis/organization

[Jane Lomax]

Well, many changes to the ontology result in changes to enrichment 
analysis results, but if you feel there are valid biological reasons for 
a parent term for 'organization' and 'biogenesis' then I'm fine with that.

Is it just the cell wall org and biogen terms that you want to unify, or 
is it others too?

Jane

Valerie Wood wrote:
> mm physiology isn't right.
>
> I still think we need a grouping term in the ontology, not just the 
> option to create these union terms in slims.
> By partitioning my cell wall terms into biogenesis and organization it 
> is  quite possible that gene sets which previously showed enrichment 
> to the "organization or biogenesis" term will no longer do so......
>
> val
>
>
> Jane Lomax wrote:
>
>> 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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>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -- 
>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Ontology-editors mailing list
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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