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Uniprot file

David Hill dph at informatics.jax.org
Fri Jan 23 04:32:29 PST 2004


MGI updates our gene annotation files at the GO site on a weekly basis. On 
our own site, the database is updated daily. As of 1/22/04 we have 4890 
genes annotated by hand with at least 1 GO annotation.

David

At 11:49 AM 1/23/2004 +0000, camon at ebi.ac.uk wrote:
>Hi Linda,
>
>The UniProt GOA dataset has integrated manual annotations from MGI,
>RGD, Flybase and SGD which do not have the ISS code.
>
>Perhaps this accounts for the differences with MGI.
>Also GOA is released monthly...so will not be totally
>in sync with MGI perhaps. Perhaps Judy and Harold
>can report on how often MGI GO data is released.
>We update monthly with what is new at that time.
>January GOA release is still pending.
>
>kind regards
>Evelyn
>
> > 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
> >>
> >>
> >>
> >> --
> >> This message is from the GOFriends moderated mailing list.  A
> >> list of public announcements and discussion of the Gene
> >> Ontology (GO) project.
> >> Problems with the list?           E-mail:
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> >>
> >
> >
> > --
> > This message is from the GOFriends moderated mailing list.  A list of
> > public
> > announcements and discussion of the Gene Ontology (GO) project.
> > Problems with the list?           E-mail: owner-gofriends at geneontology.org
> > Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
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> >
>
>
>--
>This message is from the GOFriends moderated mailing list.  A list of public
>announcements and discussion of the Gene Ontology (GO) project.
>Problems with the list?           E-mail: owner-gofriends at geneontology.org
>Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
>Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
>Web:          http://www.geneontology.org/

David Hill, Ph.D.
Senior Scientific Curator
Gene Expression Database/Gene Ontology Consortium
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609

(207)288-6430
dph at informatics.jax.org

http://www.informatics.jax.org/ 


--
This message is from the GOFriends moderated mailing list.  A list of public
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