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[Gofriends] UniProtKB-GOA release [2010-12-14]

Tony Sawford tonys at ebi.ac.uk
Tue Dec 14 05:11:50 PST 2010


UniProtKB-GOA release: 14 December 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
===========

GOA proteomes files are now created using UniProtKB proteome data

As of this latest release, UniProtKB-GOA are creating the proteomes gene 
association files using the UniProtKB proteomes data. The UniProtKB-GOA 
proteomes files are available here:
http://www.ebi.ac.uk/GOA/proteomes.html

The proteome sets provided by UniProtKB-GOA were previously based on 
those defined by the Integr8 project. Integr8 is planning to close after 
the launch of Ensembl Genomes as the next-generation interface for 
genome-scale data from non-vertebrate species. UniProtKB is taking over 
responsibility for the maintenance of the complete proteome sets, which 
can be found here:
http://www.uniprot.org/taxonomy/complete-proteomes

There are two main consequences that should be noted:

1) The proteomes are available only for those species that have a 
complete genome, as defined by INSDC. For the complete genomes, please 
see http://www.ebi.ac.uk/genomes and the NCBI Project database, 
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj

2) The entries within the proteome are the direct translation of the 
sequenced reference genome; this logic is applied to all species. Any 
species-specific rules that Integr8 used have not been propagated to the 
new sets. The proteome sets are subsets of the GOA-UniProt gene 
association file, and consequently if a protein accession is deemed not 
to be present in a particular proteome then any manual annotations made 
to this protein will not be visible in the proteome set; they will, 
however, still be available from the GOA-UniProt gene association file.


Compliments of the season,
UniProtKB-GOA Production



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