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[Gofriends] UniProtKB-GOA release [2010-06-03]

Tony Sawford tonys at ebi.ac.uk
Thu Jun 3 05:20:17 PDT 2010


UniProtKB-GOA release: 03 June 2010
===================================

UniProtKB-GOA (UniProtKB GO Annotation at EBI) is a project run by the 
European Bioinformatics Institute that provides 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.


Latest news
===========

1. Addition of annotations from CGD, Plasmodium falciparum GeneDB and PAMGO
2. New files provided describing specifically associations and 
annotation object data for the UniProtKB gene association file.
3. Change in contents of column 1 in all GOA-UniProtKB gene association 
files.

1. We are pleased to announce that this release of UniProtKB-GOA gene
association files includes manual annotations for Candida albicans,
Plasmodium falciparum and Agrobacterium tumefaciens UniProtKB accessions 
that have been created by the Candida Genome Database
(http://www.candidagenome.org/), Plasmodium falciparum GeneDB
(http://www.genedb.org/genedb/malaria) and Agrobacterium Genome
Consortium, PAMGO project (http://www.agrobacterium.org/) respectively,
from files these groups have submitted to the GO Consortium.

2. The UniProtKB-GOA group is making available two new files that have
been generated from gene_association.goa_uniprot. These files have
split between them the information specfically required to describe a GO 
annotation (gp_association.goa_uniprot) and to describe the proteins
for which annotations are provided (gp_information.goa_uniprot). Use of 
these two files instead of the gene association file has the advantage 
of reduced redundancy in the information supplied, resulting in a 
combined size of 126MB less than the gene_association.goa_uniprot file. 
However the format of these two files is subject to ongoing discussions 
by the GO Consortium, so their exact format may change over time. 
Readmes to describe the format of these files are available from the ftp 
site, alongside these two files. Files can be downloaded from:

ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_association.goa_uniprot.gz
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_information.goa_uniprot.gz

3. The contents of column 1 (DB) of all UniProtKB-GOA gene association
files has changed in this release, so that UniProtKB accession numbers
are only identified by the namespace 'UniProtKB' instead of the previous 
values of either: 'UniProtKB/TrEMBL' or 'UniProtKB/Swiss-Prot'. This 
change has occurred in response to requests from GO tool providers. 
However the new gp_information.goa_uniprot.gz file described above does 
contain the UniProtKB subset (Swiss-Prot/TrEMBL) information in column 2 
for all UniProtKB proteins that have been GO annotated.

Regards,
UniProtKB-GOA Production




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