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[Gofriends] September 2008 GOA release

Daniel Barrell dbarrell at ebi.ac.uk
Thu Sep 18 08:06:40 PDT 2008


GOA releases: September 2008
============================

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

		(the last two will be updated overnight)

For further information read: http://www.ebi.ac.uk/GOA or contact
goa at ebi.ac.uk.


NEWS:
=====

**GOA gene association file format changes**

The GOA group has made changes to the contents of columns 3, 10 and
11 in all GOA gene association files except gene_association.goa_pdb.gz.
The changes are outlined below and will ensure that the format of the 
affected columns is in line with GO Consortium requirements. While the 
ordering of identifiers in these columns will change, no identifiers 
will be removed.

*Column 3 (DB_Object_Symbol)*
Previous content: UniProt identifier (e.g. PRG4_HUMAN)
New content: Primary gene symbol when available (e.g. PRG4),
otherwise contains locus name or will repeat the value present in
column 2 (either a UniProtKB accession, IPI, Ensembl, VEGA, HINV, TAIR
or RefSeq peptide identifier).

*Column 10 (DB_Object_Name)*
Previous content: A list of gene symbols and protein name. (e.g. PRG4,
MSF, SZP: Proteoglycan-4 precursor)
New content: protein name only when available (e.g. Proteoglycan-4
precursor). Otherwise left blank.

Column 11 (Synonym)
Previous content: IPI identifiers when available (e.g. IPI00024825)
New content: A pipe-delimited list of alternative gene symbol
synonyms, IPI and UniProtKB identifiers (e.g.
MSF|SZP|IPI00024825|PRG4_HUMAN).



***New annotation source: Human Protein Atlas***

GOA now contains human protein subcellular location experimental data 
from immunofluorescence studies. See the Human Protein Atlas website:

http://www.proteinatlas.org/data/go_if_loc.php




Regards

The UniProt GOA Team

















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