[Go] Composition of the generic GO slim

[Emily Dimmer]

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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    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