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December 2006 GOA release

Daniel Barrell dbarrell at ebi.ac.uk
Tue Dec 12 07:19:45 PST 2006


GOA releases: December 2006
===========================

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.

GOA News update:
*****************

We are pleased to announce that in collaboration with the Ensembl group,
GOA is able to offer a new electronic GO annotation method, providing an
additional 59,424 annotations to the human, mouse, rat, Drosophila
melanogaster and Anopheles gambiae proteomes.

Using the gene orthology obtained from the Ensembl Compara system, GO
terms from a source species have been projected onto one or more target
species.  Only one to one and apparent one to one orthologies are used,
and only manually-annotated GO terms with an evidence type of IDA, IEP,
IGI, IMP or IPI are projected. GO annotations using this technique will
receive the evidence code 'IEA' (Inferred from Electronic Anotation). 
The projections and the resulting annotations will be updated monthly. 
In the gene association files, the Ensembl protein identifier of the 
annotation source will be indicated in column 8 ('With') and column 15 
will contain the value 'Ensembl'.

In addition, the format of column 6 (DB:Reference) has changed for all
electronic (IEA) annotations. Alongside the keyword stating the GOA 
method applied, a GO_REF identifier referencing a full description this 
method is now also present. These two values are separated by a pipe 
symbol. Values in this field for 'IEA'-evidenced annotations will be one 
of the following:

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

The full descriptions referenced by the GO_REF identifier can be found at:
http://www.geneontology.org/doc/GO.references


Please note that the version of the GOA UniProt gene association file
available from the GO Consortium ftp site (ftp.geneontology.org)  has
been filtered to remove annotations for those species where a different
Consortium group is primarily responsible for providing GO annotations.
If you would like to download an unfiltered GOA UniProt gene association
file, please use either the GOA ftp site:

ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz


Or the submissions folder in the GO Consortium ftp site:

ftp://ftp.geneontology.org/pub/go/gene-associations/submission/gene_association.goa_uniprot.gz



Please look at our README
(ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README) for further
information on the contents of the GOA gene association files.

Species which have been filtered out of the
gene_association.goa_uniprot.gz file on the GO Consortium site include:


Danio rerio
Drosophila melanogaster
Mus musculus
Rattus norvegicus

Arabidopsis thaliana
All rice species

Bacillus anthracis str. Ames
Campylobacter jejuni RM1221
Candida albicans
Caenorhabditis elegans
Coxiella burnetii RSA 493
Dehalococcoides ethenogenes 195
Dictyostelium sp., Dictyostelium discoideum
Geobacter sulfurreducens PCA
Glossina morsitans morsitans
Leishmania major
Listeria monocytogenes str. 4b F2365
Methylococcus capsulatus str. Bath
Pseudomonas syringae pv. tomato str. DC3000
Plasmodium falciparum
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Shewanella oneidensis MR-1
Silicibacter pomeroyi DSS-3
Trypanosoma brucei
Vibrio cholerae O1 biovar eltor

(Further information on this filtering script can be found at:
http://www.geneontology.org/GO.annotation.shtml#file).


Regards

The UniProt GOA Team


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