[Go] Composition of the generic GO slim

[Judith Blake]

My experience is somewhat like that of Val's.  When people here at Jax 
want to make use of a GO-Slim for data comparison, they usually have a 
reason for selecting high-level terms.  Also, there is the MGI GO-slim 
that reflects general mammalian interests.  So maybe a generic slim 
isn't that useful ... or maybe it is useful for some purposes.
http://www.informatics.jax.org/gotools/MGI_GO_Slim.html

Judy


Judy

Valerie Wood wrote:
> I also don't find any of the generic slims so useful so I always create 
> my own. They  don't provide good coverage (lots of genes with process 
> terms are omitted excluded from the slims completely, and as you say 
> many terms biologists would expect as high level grouping terms are 
> missing).
>
> Val
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>
>
> Emily Dimmer wrote:
>   
>> Hi,
>>
>>  From replying to a user request, I've just been having a quick look at 
>> the composition of the generic GO slim, and relating the GO terms 
>> included to the number of annotations displayed by AmiGO.
>>
>> Should, for instance, the 'cell recognition' term still be included in 
>> the generic GO slim? - it has only been annotated to 182 gene products, 
>> whereas its sibling terms: 'cell division', 'cell cycle' and 'cell 
>> motility', have not been included even though they (directly or 
>> indirectly) have been annotated to more than 1,200 gene products each. 
>> Similarly, the term 'cytoplasm organization and biogenesis' is in the GO 
>> slim but only has 113 gps annotated, whereas the 'membrane organisation 
>> and biogenesis' term has been annotated to 1,509 gps.
>>
>> I was just wondering what the goal of the generic GO slim is... if terms 
>> are selected on the basis that as many annotated gene products from 
>> different organisms should get mapped to descriptive GO terms before 
>> they are caught by the BP, MF, CC root terms (while also providing a 
>> full selection of terms across the whole GO vocabulary), should we think 
>> of reviewing its some of its composition in relation to overall 
>> annotation frequency? Or should the GO slim be kept as stable as possible?
>>
>> Cheers,
>> Emily
>>
>>   
>>     
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