[Ontology-editors] another question about biogenesis/organization

Valerie Wood val at sanger.ac.uk
Mon Jun 29 02:59:25 PDT 2009 

 > 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
>>
>>
>
>



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