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January 2007 GOA release

Ben Hitz hitz at genome.Stanford.EDU
Fri Feb 2 13:32:49 PST 2007


I dont think we load these files at all.  If the errors were  
propagated to the gene_assocation files and/or gp2protein files, then  
the data on godatabase.org is also in error.

Ben
>
> Hi!  Did this error affect the 200701 data published at
>
> http://archive.godatabase.org
>
> ?
>
> Regards,
>
> Gabriel
>
>
> On 2007.02.02 Fri, at 10:57, Daniel Barrell wrote:
>
>> Hi,
>>
>> There was a bug which affected the proteome sets available here:
>>
>> ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/
>>
>> This meant that files at this location were missing annotations.   
>> This is now fixed and the new files have been uploaded.
>>
>> Regards,
>>
>> Daniel
>>
>> Daniel Barrell wrote:
>>> GOA releases: January 2007
>>> ===========================
>>> GOA (GO Annotation at EBI) is a project run by the European  
>>> Bioinformatics
>>> Institute that aims to provide assignments of gene products to  
>>> the Gene
>>> Ontology (GO) resource.
>>> The data can be obtained via:
>>>            EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
>>>            EBI SRS: http://srs.ebi.ac.uk. Search GOA data library
>>>            GO FTP: ftp://ftp.geneontology.org/pub/go/gene- 
>>> associations/
>>>            GO CVS: http://www.geneontology.org/GO.CVS.help.html
>>> For further information read: http://www.ebi.ac.uk/GOA
>>> or contact goa at ebi.ac.uk.
>>> GOA News update:
>>> *****************
>>> Please note that the version of the GOA UniProt gene association  
>>> file
>>> available from the GO Consortium ftp site (ftp.geneontology.org)   
>>> has
>>> been filtered to remove annotations for those species where a  
>>> different
>>> Consortium group is primarily responsible for providing GO  
>>> annotations.
>>> If you would like to download an unfiltered GOA UniProt gene  
>>> association
>>> file, please use either the GOA ftp site:
>>> ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/ 
>>> gene_association.goa_uniprot.gz Or the submissions folder in the  
>>> GO Consortium ftp site:
>>> ftp://ftp.geneontology.org/pub/go/gene-associations/submission/ 
>>> gene_association.goa_uniprot.gz Please look at our README
>>> (ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README) for  
>>> further
>>> information on the contents of the GOA gene association files.
>>> Species which have been filtered out of the
>>> gene_association.goa_uniprot.gz file on the GO Consortium site  
>>> include:
>>> Danio rerio
>>> Drosophila melanogaster
>>> Mus musculus
>>> Rattus norvegicus
>>> Arabidopsis thaliana
>>> All rice species
>>> Bacillus anthracis str. Ames
>>> Campylobacter jejuni RM1221
>>> Candida albicans
>>> Caenorhabditis elegans
>>> Coxiella burnetii RSA 493
>>> Dehalococcoides ethenogenes 195
>>> Dictyostelium sp., Dictyostelium discoideum
>>> Geobacter sulfurreducens PCA
>>> Glossina morsitans morsitans
>>> Leishmania major
>>> Listeria monocytogenes str. 4b F2365
>>> Methylococcus capsulatus str. Bath
>>> Pseudomonas syringae pv. tomato str. DC3000
>>> Plasmodium falciparum
>>> Saccharomyces cerevisiae
>>> Schizosaccharomyces pombe
>>> Shewanella oneidensis MR-1
>>> Silicibacter pomeroyi DSS-3
>>> Trypanosoma brucei
>>> Vibrio cholerae O1 biovar eltor
>>> (Further information on this filtering script can be found at:
>>> http://www.geneontology.org/GO.annotation.shtml#file).
>>> Regards
>>> The UniProt GOA Team
>>> -- 
>>> 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- 
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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- 
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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/

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu




--
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