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Uniprot file

Daniel Barrell dbarrell at ebi.ac.uk
Fri Jan 23 05:13:05 PST 2004


As an aside, GOA also filters external 'NOT' annotation, annotation that 
can't be mapped to a UniProt entry and manual annotation without a valid 
PubMed reference.  This will also affect numbers.

Linda - I'm a little confused about your numbers, but upon double 
checking I think you have them back to front. GOA incorporated mappings 
to 3002 MGI annotated genes.

Regards,

Daniel


David Hill wrote:

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

-- 

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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