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Uniprot file

Hannick, Linda lhannick at tigr.org
Thu Jan 22 13:21:43 PST 2004


Hi,
I need some guidance about the UNIPROT set.  We would like to
non-redundify (how's that for a verb!) the peptide set that we use as
our comparison set.  Studying the tables at GOA does not answer the
following questions.

It is not clear to me whether the GOA total of manual GO annotations
(26433 proteins) contains all of the accessions in the manual GO
annotations done by MGI, RGD and Proteome.  

Why is the number in "manual GO annotation by MGI" at GOA (5945
proteins) different than the number in the MGI table (3002 proteins)?
If we download all of the manual GO associations (and sequences) that
are in the GOA list, will there be manual GO associations at MGI that we
will have missed?  I think the question really is: are the UNIPROT GO
associations kept in sync with the versions of MGI, etc?

Thanks,
Linda




~~~~~~~~~~~~~~~~~~~~~~~~~~~
Linda I. Hannick, Ph.D.
Bioinformatics Analyst
The Institute for Genomic Research
301-795-7857 voice
301-838-0228 fax



> -----Original Message-----
> From: owner-gofriends at genome.stanford.edu 
> [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of 
> Daniel Barrell
> Sent: Wednesday, January 21, 2004 6:37 AM
> To: DERET Sophie
> Cc: gofriends at genome.stanford.edu
> Subject: Re: Uniprot file
> 
> 
> 
> Hi Sophie,
> 
> gene_association.goa_uniprot.gz contains all species from The UniProt 
> knowledgebase (TrEMBL/Swiss-Prot/PIR) - 61962 species (see 
> http://www.ebi.ac.uk/GOA/SPTR_release.html).  You can filter 
> this file 
> by taxon id if necessary.  The GOA project also provides the 
> following 
> species specific files:
> 
> gene_association.goa_human
> gene_association.goa_mouse
> gene_association.goa_rat
> 
> Information on these can be found here:
> 
> ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README
> 
> Other groups provide model organism database specific files here:
> 
> http://www.geneontology.org/GO.current.annotations.shtml
> 
> You will notice that the GOA files are also available from 
> this link.  
> With regard to your question about GO:0005504, could you 
> expand a little 
> on this?  I'm unsure what you mean.
> 
> Regards,
> 
> Daniel
> 
> 
> 
> DERET Sophie wrote:
> 
> > Dear GO friends,
> >
> >  
> >
> > I downloaded gene_association.goa_uniprot.gz file from
> > ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/.
> >
> > I have question about contents of this file:
> >
> > - is there only one file for all species (human, rat, pig...)?
> >
> > - in this file, I didn't find all GO ID included in
> > gene_association.goa_human (example: GO: 0005504), why?
> >
> >  
> >
> > Thanks a lot for your response.
> >
> >  
> >
> > Sophie
> >
> 
> -- 
> 
> Daniel Barrell
> EMBL - The EBI
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> Phone: +44 (0)1223 492551
> Email: dbarrell at ebi.ac.uk
> 
> 
> 
> --
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