[go-friends] UniProtKB-GOA release [2011-07-28]

[Tony Sawford]

UniProtKB-GOA release: 28 July 2011
===================================

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. With the imminent closure of the International Protein Index (IPI), 
we would like to alert users of the Human, Mouse, Rat, Zebrafish, 
Chicken and Cow UniProt GO annotation files (files named: 
gene_association.goa_[species], e.g., gene_association.goa_human) that 
our July GO annotation release now uses UniProt Complete Proteome sets 
to determine the protein composition of these files. Further information 
on UniProt Complete Proteome sets is available here: 
http://www.uniprot.org/faq/15

This change has had a dramatic affect on the gene_association.goa_human 
file, which has increase in annotation count by 43.7% , as the file now 
includes GO annotations both to reviewed (Swiss-Prot) and unreviewed 
(TrEMBL) UniProtKB accessions. Any user wishing to only identify the 
reviewed (Swiss-Prot) UniProt protein annotation subset will be able 
continue to do so using the information supplied in the 
gp_information.goa_uniprot file, which can be found here: 
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_information.goa_uniprot.gz
Alternatively, users can download the reviewed UniProtKB human GO 
annotation set from the UniProt QuickGO browser using this link: 
http://www.ebi.ac.uk/QuickGO/GAnnotation?tax=9606&db=UniProtKB%2FSwiss-Prot

Users of the Zebrafish species-specific gene association file will, 
however, notice a decrease in annotations this release, caused by major 
changes to the Ensembl Zebrafish ENSP identifier set that has resulted 
in a decreased set of electronic GO annotations obtained from the 
application of Ensembl Compara orthology data, as well as a decrease in 
ZFIN manual GO annotations caused by differences in the set of UniProtKB 
accessions selected for the Zebrafish UniProtKB proteome set and those 
currently mapped to ZFIN identifiers.

2. An additional restriction on the HAMAP2GO electronic GO annotation 
pipeline, filtering out all HAMAP2GO predictions for proteins in the 
Metazoan kingdom, has enabled us to remove incorrect GO annotation 
predictions for a number of species.

3. Species-specific UniProt GO annotation gene association files that 
include a filtering step to remove redundant electronic GO annotation 
predictions are now available from the GOA ftp site for the UniProt 
Complete Proteome sets of Dictyostellium discoideum 
(gene_association.goa_dicty.gz), Canis familiaris 
(gene_association.goa_dog.gz), Drosophila melanogaster 
(gene_association.goa_fly.gz), Caenorhabditis elegans 
(gene_association.goa_worm.gz), Saccharomyces cerevisiae 
(gene_association.goa_yeast) and Sus scrofa (gene_association.goa_pig.gz).


Regards,
UniProtKB-GOA Production