D700–D705 Nucleic Acids Research, 2012, Vol. 40, Database issue doi:10.1093/nar/gkr1029 Published online 21 November 2011 Saccharomyces Genome Database: the genomics resource of budding yeast J. Michael Cherry*, Eurie L. Hong, Craig Amundsen, Rama Balakrishnan, Gail Binkley, Esther T. Chan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Kalpana Karra, Cynthia J. Krieger, Stuart R. Miyasato, Rob S. Nash, Julie Park, Marek S. Skrzypek, Matt Simison, Shuai Weng and Edith D. Wong Department of Genetics, Stanford University, Stanford, CA, 94305-5120, USA Received September 15, 2011; Revised October 19, 2011; Accepted October 21, 2011 ABSTRACT The Saccharomyces Genome Database (SGD, http:// www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and inter- actions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use. INTRODUCTION Saccharomyces cerevisiae has been widely utilized in the exploration of biochemistry, molecular biology, cell biology and systems biology because of the ease with which it can be grown and manipulated, the extensive conservation of its genes and pathways with those of higher organisms, and the powerful genetic techniques that it offers. Many new genome-wide technologies—the creation of bar-coded systematic deletion sets; large-scale detection of protein–protein and genetic interactions and subcellular localizations; transcriptome, proteome and metabolome analysis—were ﬁrst developed using yeast before being more widely applied to other organisms. For these reasons S. cerevisiae research serves as a model for a variety of processes that occur in humans, many of which are disease-associated. Direct parallels can be drawn between the two organisms in areas such as lipid metabolism (1), the unfolded protein response (2), mitochondrial metabolism (3), prion development (4) or ageing (5), to name just a few possible examples. The core users of Saccharomyces Genome Database (SGD) include those conducting research on Saccharomyces species as well as those exploring the genetics and cellular biology of other fungal genera that are important to basic research, human health and industry. Researchers studying larger organisms, including models such as Drosophila and Caenorhabditis, as well as plants and humans, represent growing communities that look to SGD for information when their research leads to genes with similarity to one of the many that are already well characterized in yeast. Educators and students in genetics and cellular biology comprise another large com- munity that SGD serves, as do bioinformatics scientists who perform genome-wide computational analyses, for either yeast or comparative studies. In this update the organization and enhancement to the SGD resource is presented in three parts: the representa- tion and integration of experimental results into a rich biological model, new query and display tools that unlock discovery of this information, and new social media outlets to stay informed of new features and data provided by SGD. REPRESENTATION OF EXPERIMENTAL RESULTS: CAPTURING, MAINTAINING AND INTEGRATING HIGH-QUALITY ANNOTATIONS We deﬁne curation as the comprehensive and accurate manual extraction of experimental results from *To whom correspondence should be addressed. Tel: +1 650 723 7541; Email: cherry@stanford.edu The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.