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[Gofriends] GOA release [2010-04-22]

Tony Sawford tonys at ebi.ac.uk
Thu Apr 22 05:51:28 PDT 2010


GOA releases: 22 April 2010
===========================

GOA (GO Annotation at EBI) is a project run by the European Bioinformatics
Institute that provides 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:
1. GOA-UniProtKB files supplied in GAF2.0 format
2. New PDB gene association file

1. GOA-UniProtKB files supplied in GAF2.0 format
In line with GO Consortium intentions, the format of GO annotation files 
available from the UniProtKB-GOA project are now supplied in a 17-column 
GAF format (GAF2.0) instead of the previous 15 columns. This new 
association format has been prepared with the GO Consortium's 1st June 
2010 switchover date in mind, as after this date the GO Consortium's 
gene-associations ftp directory 
(ftp://ftp.geneontology.org/pub/go/gene-associations/) will only supply 
users with GAF2.0 formatted files.

However, if you require the older, 15-column GAF1.0 format for any of 
the GOA-UniProtKB files, a Perl conversion script is now made available 
at:   ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/tools/gaf_convert.pl

This script will assist users to convert any GOA-UniProtKB file from the 
newer GAF2.0 format to GAF1.0; it is used thus:

     perl gaf_convert.pl < input_file > output_file

where input_file is a GAF2.0 annotation file, and output_file is the 
generated GAF1.0 file.

The format of the new GAF2.0 annotation file is described in the GO web 
page below:
http://www.geneontology.org/GO.format.gaf-2_0.shtml

In essence, this format change means that two columns have been added to 
the end of the previous tab-delimited file format:

Column 16 (Annotation Extension). It is intended that this column will 
provide additional cross references to other ontologies that can be used 
to qualify or enhance a GO annotation. As discussions are ongoing within 
the GO Consortium as to the exact format of this field, the column is 
currently empty in all GOA-UniProtKB files.

Column 17 (Gene Product Form ID). This column will specifically identify 
which gene product is being annotated. Where possible, annotations from 
the UniProtKB-GOA group will supply isoform identifiers in column 17 to 
identify isoform-specific functionality.

It will not be mandatory for users to use the information supplied in 
columns 16 and 17; it is intended that this data will enhance the 
annotation descriptiveness, but will not radically modify the 
interpretation of the annotation information supplied in columns 1 to 15.

2. New PDB gene association file
We are pleased to include in this release a new format for the PDB gene 
association file. This file has been generated from a collaboration 
between the InterPro, PDB and UniProtKB-GOA teams, and once again is 
able to offer annotations to PDB chain identifiers. In addition, further 
sources of GO annotations are now associated with PDB chains, to provide 
a more comprehensive PDB GO annotation resource.  Manual and electronic 
GO annotations are now provided in this file from two sources:

1. where an InterPro entry matches a PDB chain, annotations supplied by 
the InterPro2GO electronic method are assigned to the chain identifier 
(for further details on this method see: 
http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002).

2. PDB chains are additionally supplied with manual and electronic GO 
annotations (excluding InterPro2GO) when a PDB chain maps with at least 
90% identity to a UniProtKB accession (more specifically with the 
UniProtKB's CHAIN feature), whereupon manual and electronic annotations 
are supplied to the PDB chain identifier from the matching UniProtKB 
accession.

Regards,
GOA Production






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