[Go] Composition of the generic GO slim

[Valerie Wood]

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



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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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
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Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe



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