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[Gofriends] March 2009 GOA release

Daniel Barrell dbarrell at ebi.ac.uk
Tue Mar 10 08:55:36 PDT 2009


GOA releases: March 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 gene_association.goa_human:
================================================

As previously announced we have changed the way we make the
gene_association.goa_human file, please read the following which is
taken from the README file:


5.  The non-redundant human proteome set
---------------------------------------------------------

In February 2009, the production of the gene_association.goa_human file
changed from using the International Protein Index (IPI) to using the
complete human proteome set available from UniProtKB/Swiss-Prot
(http://www.uniprot.org/news/2008/09/02/release).

The name and format of this human file has remained the same, however
annotations are now assigned to proteins from just the 'UniProtKB'
column 1) database source. Human IPI identifiers continue to be included
in column 11 of annotations.

In addition, new releases of the cross-references file for human IPI set
(human.xrefs.gz), will no longer be provided. Instead, identifier
apping is possible using the UniProt ID mapping file, available from:
ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz 


idmapping.dat.gz is a tab-delimited table, which includes mappings for
20 different sequence identifier types, including IPI identifiers.

A readme for this file is available from:

ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/README

Regards

The UniProt GOA Team






















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