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[go-friends] UniProt-GOA release [2016-06-08]
Tony Sawford
tonys at ebi.ac.uk
Wed Jun 8 06:13:11 PDT 2016
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
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