[Annotation] mapping genes to GO slims

[Emily Dimmer]

Hi Doug,

QuickGO can do this (http://www.ebi.ac.uk/ego/). The tool has integrated 
the GO slims the GOC maintains and also allows users to make their own 
GO slim sets. The tool also enables you to map annotations up to these 
selected GO terms, and also to exclude from this annotation set those 
annotations which have applied a certain evidence code, reference, or 
select annotations from certain annotation groups. The tool also 
includes identifier mapping capabilities (including to ZFIN identifiers).

Rachael has created a nice video tutorial on this application of 
QuickGO, which is available here:
http://www.ebi.ac.uk/ego/tutorial/QuickGO_Slim.html

Of course, as GOA doesn't currently integrate annotations from external 
groups which are IEA or ISS-evidenced, or those which do not map to an 
equivalent UniProtKB accession, so you might find that the ZFIN 
annotation set is not as complete as you might like.

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


-- 


Do you need any additional GO annotation resources?
Which proteins would you like annotated with GO?

Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html

------------------------------------------------------------------ 

    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