[Ontology-editors] another question about biogenesis/organization

Jane Lomax jane at ebi.ac.uk
Tue Jun 30 07:36:24 PDT 2009 

Okay by me.

Jane

Valerie Wood 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.
>
> I monitor the changes to high level terms and I am not aware of 
> another case where a useful high level term has "disappeared". 
> Although I am still angling to get meiotic and mitotic spindle pole 
> body organization terms back, these do not really affect current 
> enrichments and slims so drastically as the "cell wall organization 
> and biogenesis term".
>
> Most changes to the ontology result in an increase in the number of 
> annotations to a term (unless the term was incorrectly used), in which 
> case we may see a drop. Losing a useful term, I have no other 
> recollection of previousl, and definately not one which is used in slims.
>
> In pombe, the cell wall community is very active and I am worried that 
> they may no longer see this enrichment now the annotations are split 
> between 2 terms becuas the overlap is only about 1/3 of the genes to 
> each seperate term.
>
> Midori said we could have "org OR bio" can we have this until we can 
> come up with a better collective term name?
>
> Val
>
>
> Chris Mungall wrote:
>
>>
>> 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
>>>
>>>
>>
>>
>
>
>


-- 
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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