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January 2007 GOA release

Gabriel Berriz gberriz at hms.harvard.edu
Fri Feb 2 13:37:26 PST 2007


it would be useful to have at least one association that was missing  
before the error was fixed, to quickly spot any data set that is  
corrupted.

G.

On 2007.02.02 Fri, at 16:32, Ben Hitz wrote:

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


--
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