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.

YeastMine Upgrade

May 28, 2013

YeastMine, SGD’s powerful search and retrieval tool, has been upgraded to use InterMine version 1.1 software. Highlights of this release include a new format for the template results page, the addition of PantherDB and Homologene homolog data, an improved representation of Gene Ontology (GO) information, the ability to set background population within the GO enrichment widget, and an option to share lists with other users. In addition to the existing video tutorials, a new Help document describes some common queries. See an overview of these new features in the video below, New, Fun YeastMine 1.1!:

New, Fun YeastMine 1.1! from yeastgenome on Vimeo.

Filter Expression Data by Experimental Condition

December 16, 2011

Expression analysis at SGD now offers the ability to filter datasets by condition(s) or process(es) studied. A set of controlled vocabulary (CV) terms describing various perturbations associated with microarray experiments has been constructed and defined, and these terms have been used to tag the comprehensive collection of almost 400 datasets now available in SGD’s instance of SPELL (Serial Pattern of Expression Levels Locator). In this manner, datasets displayed in search results can be filtered using tags (CV terms) such as “oxidative stress” or “sporulation.” Filtering is an option for the “New Search,” “Show Expression Levels,” and “Dataset Listing” features. The SPELL interface has been provided through a collaboration with the SGD Colony at Princeton University. Special thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help in implementing the dataset tag filtering option for SPELL at SGD.

GO Slims Updated

August 12, 2011

SGD has updated its Yeast Molecular Function and Biological Process GO Slims to include additional terms. The Yeast GO Slims are a set of GO terms that best represent the major biological processes, molecular functions, and cellular components that are found in S. cerevisiae. GO Slim terms are useful in mapping precise, “granular” gene annotations to more general “high-level” terms. These terms have been selected by SGD curators based on annotation statistics and biological significance. To complement the expanded Yeast GO Slims, we have also added “generic GO-Slim” options to our GO Slim Mapper tool. The generic GO-Slim is developed and maintained by the Gene Ontology Consortium and includes fewer and higher-level terms than those provided by the Yeast GO-Slim.

The Yeast GO Slims are available for analysis via the GO Slim Mapper tool and YeastMine. Mapping of all the yeast gene products to the Yeast GO Slims is also available as a graphical view on the Genome Snapshot page and via the go_slim_mapping.tab file on the downloads site.

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