New & Noteworthy

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.

Textpresso now includes publications from 2011

June 21, 2011

The SGD full-text literature search (powered by Textpresso) has been upgraded and updated to include 58,000 papers. Textpresso now includes the ability to restrict your searches to a subset of PMIDs as well as limit the results to a specific section of a paper. The full-text literature search can be accessed via the Full-text Search link on the home page. Thanks to Arun Rangarajan and Hans-Michael Muller from Wormbase for their help upgrading the software.

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