[Gofriends] May 2009 GOA release

[Daniel Barrell]

GOA releases: May 2009
===========================

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.


Important News about intended file format changes:
==================================================

Please note that GOA is intending to implement two changes to the format 
of the gene association files that will affect annotations supplied in 
future GOA releases. These changes will affect columns 1 and 6:

1. DB field (column 1). Column 1 of the gene association file is used to 
identify the database which has supplied the sequence identifier 
displayed in column 2. Its value is very often 'UniProtKB'. However 
recent changes to other fields in the GOA gene association files have 
made it difficult for users to identify whether an UniProtKB accession 
originates from the UniProtKB/Swiss-Prot or UniProtKB/TrEMBL databases. 
Therefore it is intended that when a UniProtKB accession is provided in 
column 2, column 1 will in future display either 'UniProtKB/Swiss-Prot' 
or 'UniProtKB/TrEMBL'.

2. DB:Reference field (column 6). Changes to this field were advertised 
last month, however it has not been possible to carry out the required 
work in time for this release. Therefore the changes outlined again 
below will be implemented in the next GOA file release:

Currently annotation lines produced by electronic methods (as indicated 
by the presence of the 'IEA' evidence code in column 7) contain two 
identifiers piped together in the reference column; an internal GOA 
keyword (e.g. GOA:interpro) and a GO reference identifier (e.g. 
GO_REF:0000002). As of the next file release, the GOA internal reference 
(e.g. GOA:interpro) and pipe will be removed from this field, so that 
only a GO_REF identifier will be provided.

Full descriptions of the methods referenced by a GO reference identifier 
can be found at:  http://www.geneontology.org/cgi-bin/references.cgi

This format change will effect all annotation lines with the following 
reference field contents:

GOA:interpro|GO_REF:0000002
GOA:hamap|GO_REF:0000020
GOA:spkw|GO_REF:0000004
GOA:spec|GO_REF:0000003
GOA:compara|GO_REF:0000019
GOA:spsl|GO_REF:0000023


Regards

The UniProt GOA Team