[Annotation] mapping genes to GO slims

[Emily Dimmer]

Alternatively, GO slimmer appears also to do exactly what you need; 
heres an extract from a recent GO help email that Midori sent out:

The database used by AmiGO and the GO Slimmer only include manually 
curated annotations. If you want to use the GO Slimmer with gene 
products that have electronic annotations, you can upload an annotation 
file.

You can download files from 
http://www.geneontology.org/GO.current.annotations.shtml.

To upload a file into the GO slimmer, choose 'gene association file' 
from the pull-down menu (where it says 'OR upload a') and choose your file.

...although I'd still recommend QuickGO for creating/adapting a GO slim :-)

Cheers,
Emily


Doug Howe wrote:
> Perhaps the most repeated question on the lists:
> Does anyone have a bead on the current best way to map a list of genes 
> (symbols or MOD IDs) to a GO slim, with the ability to include and 
> exclude IEA annotations?
>
> AmiGO has some of this, but it isn't clear to me how/if I could 
> provide the ZFIN GAF file along with a list of target genes of 
> interest so the IEAs would be included in the analysis?
>
> Any recommendations?
>
> -Doug
>
> Doug Howe, Ph.D.
> Scientific Curator
> Zebrafish Nomenclature Coordinator
> Zebrafish Information Network
> 541-346-0120
> dhowe at zfin.org
>
>
>
>
> _______________________________________________
> Annotation mailing list
> Annotation at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/annotation


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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