New & Noteworthy

Changes to the SGD GAF File of Gene Ontology Annotations

March 11, 2014

The SGD Gene Associations file (GAF; gene_association.sgd) contains Gene Ontology (GO) annotations for all yeast genes, in a standard file format specified by the GO Consortium. We are changing the taxon identifier in this file to be consistent with the reference genome sequence at GenBank and protein entries at UniProt.

Until now, the taxon identifier in column 13 of SGD’s GAF has been 4932, which refers to Saccharomyces cerevisiae in general rather than to a specific S. cerevisiae strain. Starting March 8th, 2014, we have changed this to taxon ID 559292, which is specific to the S288C strain used for the S. cerevisiae reference genome sequence.

Please note that the taxon ID 559292 merely reflects the sequence (genome) to which the geneIDs in column 2 are mapped. SGD will continue to capture gene functions (GO annotations) for all strains of S. cerevisiae. Please contact us if you have any questions.
The S. cerevisiae GO annotations (GAF) can be downloaded from SGD’s Downloads site.