[Ontology-editors] another question about biogenesis/organization

[Chris Mungall]

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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> 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
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>