[Ontology-editors] another question about biogenesis/organization

Midori Harris midori at ebi.ac.uk
Tue Jun 30 07:43:45 PDT 2009 

David has said he prefers to avoid conjunctions in term names wherever 
possible, but last time I talked to him he couldn't think of a better name 
for this term either. So I think as long as it's understood that we want 
to come up with a different, OR-free, name some time, we can tolerate 'org 
or biogen' in the meantime.

m

On Tue, 30 Jun 2009, Jane Lomax wrote:

> 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
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> 
>
>
>

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