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

Ranjana Kishore ranjana at caltech.edu
Wed Apr 16 13:11:26 PDT 2014


Hi Rachael,
We use the UniProt file 9.C_elegans.goa at ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/.  There will be some changes in pipeline/scripts that we will have to make on our side, if the format changes, but given sufficient advance notice we can be reay.  And of course, if there are ready scripts available for conversions, that will help.

Thanks
Ranjana 
WormBase


On Apr 16, 2014, at 4:10 AM, Rachael Huntley <huntley at ebi.ac.uk> wrote:

> 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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