[go-friends] UniProt-GOA release [2016-06-08]

[Tony Sawford]

UniProt-GOA release: 08 June 2016
=================================

UniProt-GOA (UniProt GO Annotation) is a project run by the UniProt
group 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/

           GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/

           GO SVN: http://www.geneontology.org/GO.svn.help.shtml

For further information read: http://www.ebi.ac.uk/GOA or contact
goa at ebi.ac.uk.

Latest News
===========

Changes to GOA annotation files
===============================

Following discussions with the GO Consortium, we have made some changes 
to the set of annotation files that we publish.

Note that in the following text, <species> is one of: human, chicken, 
cow, pig, dog, mouse, rat, arabidopsis, zebrafish, worm, yeast, fly, or 
dicty


i) Changes to species-specific annotation sets

With effect from this GOA release, we now publish the following four 
annotation sets per species, which we provide in both GAF and GPAD 
format, the format being indicated by the file suffix:

- goa_<species>.[gaf|gpa]         - annotations to canonical accessions 
from the UniProt reference proteome
- goa_<species>_isoform.[gaf|gpa] - annotations to isoforms from the 
UniProt reference proteome
- goa_<species>_complex.[gaf|gpa] - annotations to complexes
- goa_<species>_rna.[gaf|gpa]     - annotations to RNAs

Note that annotations to proteins that are not part of the UniProt 
reference proteome for a species are still available in the full 
goa_uniprot annotation set (goa_uniprot_all.[gaf|gpa]).

These files replace the old species-specific annotation sets:

- gene_association.goa_<species>
- gp_association.goa_<species>
- gene_association.goa_ref_<species>
- gp_association.goa_ref_<species>


ii) Changes to species-specific metadata files

Metadata files contain information (name, symbol, synonyms, etc) about 
both annotated and unannotated gene products.

With effect from this GOA release, we now publish the following four 
metadata files per species:

- goa_<species>.gpi - metadata for canonical accessions from the UniProt 
reference proteome (GCRP) for the species
- goa_<species>_isoform.gpi - metadata for isoforms from the UniProt GCRP
- goa_<species>_complex.gpi - metadata for complexes
- goa_<species>_rna.gpi - metadata for RNAs

These files contain entries for all gene products in that particular 
category, whether they are annotated or not, and they replace the old 
species-specific metadata files, gp_information.goa_<species> and 
gp_information.goa_ref_<species>.


iii) Changes to other annotation sets

For consistency with the new naming convention used for the 
species-specific files, we have changed the names of the following 
files; their content, however, remains unchanged:

- gene_association.goa_uniprot     is now goa_uniprot_all.gaf
- gp_association.goa_uniprot       is now goa_uniprot_all.gpa
- gene_association.goa_ref_uniprot is now goa_uniprot_gcrp.gaf
- gp_association.goa_ref_uniprot   is now goa_uniprot_gcrp.gpa
- gp_information.goa_uniprot       is now goa_uniprot_all.gpi
- gp_information.goa_ref_uniprot   is now goa_uniprot_gcrp.gpi


If you have any comments or questions about these changes, please email 
us at goa at ebi.ac.uk.


Regards,
UniProt-GOA Production