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[go-friends] Usage of UniProt Gene Association Files for GO annotation

Rachael Huntley huntley at ebi.ac.uk
Wed Apr 16 04:10:15 PDT 2014


Hello,

If you make use of the UniProt gene association files (GAF), please read on.

As the GO Consortium now has an improved annotation file format 
(combining Gene Product Association Data, "GPAD" and Gene Product
Information, "GPI" files), which is designed to replace the Gene 
Association File format (GAF), UniProt are investigating the impact of
stopping the production of GAF format files and supplying only the GPAD 
and GPI format files.

We encourage all users who retrieve UniProt GO annotations to obtain 
these annotations from the GPAD/GPI files (available from UniProt-GOA at
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/) rather than GAF files, but we 
would like to know who currently makes use of our GAF format files (Gene
Association Files) that are available from the following locations:

    - the UniProt-GOA ftp site (ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/)
    - the GO Consortium website
(http://www.geneontology.org/GO.downloads.annotations.shtml)
    - the GO Consortium ftp site
(ftp://ftp.geneontology.org/pub/go/gene-associations/)

In order for you to recognise if you are using GAF files, they are named 
according to the following convention: gene_association.goa_<species> or
gene_association.goa_ref_<species>.

The data included in the Gene Association Files will still be available 
in a couple of different ways. Firstly, the GO Consortium will provide a
conversion script, that converts between GAF and GPAD and back again. 
Secondly, annotations can be downloaded manually
or programmatically in GAF format from the QuickGO browser 
(www.ebi.ac.uk/QuickGO). N.B. currently it is not possible to download
an equivalent to the gene_association.goa_ref_<species> file, which 
contain annotations to proteins in the UniProt reference proteomes,
however this will be possible when the new and improved QuickGO 
interface is released later this year.

*If you make use of the UniProt GAF files**, please could you contact us 
with details of which files you use, how you access the files and 
whether you**
**think the removal of these files might cause you problems.*

If we decide on any such change, it will be announced well ahead of time 
in order for users to make any updates to their working practices and it 
will only take effect once all equivalent files can be downloaded from 
the new QuickGO interface.

Many thanks for your attention.

Best wishes,
Rachael Huntley on behalf of the UniProt GO Annotation project.
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