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[Gofriends] Reminder: Changes to the GO Consortium gene association file format
edimmer at ebi.ac.uk
Fri May 28 10:07:24 PDT 2010
Just a reminder that all gene association files supplied from the GO
Consortium site will be made available in GAF2.0 format from the 1st of
On 02/03/2010 16:05, edimmer at ebi.ac.uk wrote:
> Dear All,
> On the 1st of June 2010, the format of GO annotation files available from
> the GO Consortium web and ftp site will change, with files being supplied
> in a 17-column GAF format (GAF2.0) instead of the current 15 columns.
> The format of the new annotation file is described in the GO web page below:
> In essence, this format change means that two columns will be added to the
> end of the current tab-delimited file format:
> Column 16 (Annotation Extension). This column will provide additional
> cross references to other ontologies that can be used to qualify or
> enhance a GO annotation. Cross-references will be prefaced by an
> appropriate GO relationship and references to multiple ontologies will be
> provided. Targets of certain processes or functions can also be included
> in this field to indicate the gene, gene product, or chemical involved.
> The finalstructure of data in this field is currently being discussed. As
> the Consortium agrees on the presentation of certain types of data in
> column 16, details will be announced to the GO Friends email list. It
> will be optional for GO Consortium annotation groups to supply data in
> this column.
> Column 17 (Gene Product Form ID). This column will specifically identify
> which gene product is being annotated. For example, it may include protein
> sequence identifiers that specify distinct proteins variants produced by
> differential splicing, alternative translational starts,
> post-translational cleavage or post-translational modification.
> Identifiers for functional RNAs can also be included in this column. The
> addition of this new column means that the DB_Object_ID (column 2) will
> always reference a gene or protein identifier that has a 1-1
> correspondence to a gene. It will be optional for GO Consortium
> annotation groups to supply data in this column.
> It will not be mandatory for users to use the information supplied in
> columns 16 and 17; this data will enhance the annotation descriptiveness,
> but will not radically modify the interpretation of the annotation
> information supplied in columns 1 to 15.
> Before the 1st June switchover date, the GO Consortium's gene-associations
> ftp directory (ftp://ftp.geneontology.org/pub/go/gene-associations/) will
> only supply users with GAF1.0 formatted files. On the 1st of June, the
> gene-associations directory will switch to supplying GAF2.0 files. Please
> ensure that your gene association parsers are updated to accept this
> format change by this date.
> Best regards,
> GO Consortium managers
> Gofriends mailing list
> Gofriends at geneontology.org
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