[Go] Composition of the generic GO slim

[Ben Hitz]

Emily -
I have interest in working on the generic go slim; I need it (or  
something similar) to define graphics for an interaction network.

Ben


On Apr 30, 2008, at 10:03 AM, 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
>
> -- 
>
>
>
> ------------------------------------------------------------------
>
>    Emily Dimmer Ph.D.
>    GOA Coordinator
>    EMBL-EBI
>    Wellcome Trust Genome Campus
>    Hinxton
>    Cambridge CB10 1SD, U.K.
>    Tel:     +44 1223 494654
>    Fax:    +44 1223 494468
>    email:  edimmer at ebi.ac.uk
>    URL:    http://www.ebi.ac.uk/goa
>
>
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--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu