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[Gofriends] July 2008 GOA release

Daniel Barrell dbarrell at ebi.ac.uk
Fri Jul 4 03:50:40 PDT 2008


GOA releases: July 2008
============================

[Please see below for important proposed form at change]

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.

**Proposed GOA gene association file format change**

The GOA group is intending to change the contents of columns 3, 10 and
11 in all GOA gene association files except gene_association.goa_pdb.gz.
The changes being proposed 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.  These changes will come into
effect at the end of July (Release 65 of GOA UniProt, i.e. the next 
release of GOA).

*Column 3 (DB_Object_Symbol)*
Current content: UniProt identifier (e.g. PRG4_HUMAN)
Future content: Primary gene symbol when available (e.g. PRG4),
otherwise will contain 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)*
Current content: A list of gene symbols and protein name. (e.g. PRG4,
MSF, SZP: Proteoglycan-4 precursor)
Future content: protein name only when available (e.g. Proteoglycan-4
precursor). Otherwise will be left blank.

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

Please contact us if you have any concerns about these proposed changes.

Regards

The UniProt GOA Team
















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