[Ontology-editors] another question about biogenesis/organization

Chris Mungall cjm at berkeleybop.org
Fri Jun 26 14:44:43 PDT 2009 

tangent to one of my favourite i.e. repeatedly stated topics:

we really need to be collecting datasets with which we can quantify  
the effects of changes in the ontology. This can be quite simple - a  
bag of gene IDs associated with a publication ID (maybe this could be  
integrated with the 'database' underpinning http://www.geneontology.org/cgi-bin/biblio.cgi)

This is sufficient to able to measure the effects of historic or  
proposed changes on the ontology. A tool would take two versions of  
the ontology plus the above dataset and spit out a possibly very  
interesting answer.

Of course, hand curating this dataset would be tedious and time  
consuming but I bet there is someway to get the majority of the  
information out of expression databases etc

But in the absence of such a tool and even with such a tool we should  
of course rely on biologists intuition about what makes a good  
abstraction.

On Jun 26, 2009, at 5:35 AM, Jane Lomax wrote:

> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>
>
> -- 
> 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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