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[gofriends] November 2007 GOA release

Daniel Barrell dbarrell at ebi.ac.uk
Wed Nov 14 06:46:10 PST 2007


GOA releases: November 2007
============================

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.

GOA News Update:
*****************

New Subcellular Location2GO mapping (spsl2go)

The GOA group are pleased to announce that in collaboration with 
Serenella Ferro Rojas of the Swiss Institute of Bioinformatics, we are 
able to offer a new external database mapping file. So far, 269 
Subcellular Location terms from the Comment (CC) lines of UniProtKB 
entries have been manually mapped to GO terms. The new mapping has been 
applied electronically to enhance the electronic (IEA coded) GO 
annotation in our latest GOA release. This mapping has provided 418,185 
new associations with 396,734 proteins.
The spsl2go mapping file is available from the GOA ftp site 
(ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/spsl2go) and the 
Gene Ontology Consortium website 
(http://www.geneontology.org/external2go/spsl2go). The GO reference for 
this mapping is GO_REF:0000023.



PRSF2GO mapping file now available

This month, the GOA group has created a PRSF2GO mapping file. This file 
is a subset of the InterPro2GO mapping, with PRSF identifiers used 
instead of InterPro identifiers.
The prsf2go mapping file is available from the GOA ftp site 
(ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/prsf2go) and the 
Gene Ontology Consortium website 
(http://www.geneontology.org/external2go/prsf2go).



Ensembl Compara pipeline

This month, the Ensembl Compara electronic annotation pipeline will 
provide annotations to an increased set of species, including macaque, 
chimpanzee, guinea pig, Xenopus, Tetradon, Fugu, zebrafish and Aedes 
aegypti.
For full details of this method, please see: 
http://www.ebi.ac.uk/goa/compara_go_annotations.html



External Dates

Annotation dates supplied in column 14 of the GOA gene association files 
have now been corrected for annotations integrated from external model 
organism databases.



GOA Survey

The GOA group now has added a short user survey to our website, which we 
invite you to complete, especially if:
- you have set of proteins that you would like to suggest to be 
prioritized for manual annotation?
- you would like to join our expert panel to review a specified set of 
fully manually-annotated proteins?
- there are additional files that GOA could supply that you would find 
useful?
The survey is available at: http://www.ebi.ac.uk/GOA/contactus.html


Regards

The UniProt GOA Team





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