Dianna G. Fisk

The Gene Ontology (GO) database and informatics resource.

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Saccharomyces Genome Database: the genomics resource of budding yeast

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 interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use.

Saccharomyces Genome Database.

Publisher Summary The goal of the Saccharomyces Genome Database (SGD) is to provide information about the genome of this yeast, the genes it encodes, and their biological functions. The genome sequence of S. cerevisiae provides the structure around which information in SGD is organized; value is added to the sequence by careful biological annotation drawn from a number of sources. SGD curates and stores information about budding yeast DNA and protein sequences, genetics, cell biology, and the associated community of researchers. SGD also provides search and analysis tools designed to help researchers mine the data for pieces or patterns of biological information relevant to their interests. A continuing challenge for the staff of SGD is to present up-to-date information about yeast genes in a format that is intuitive and useful to biomedical researchers, while responding to the needs of this community by providing resources and tools for exploring the data in new ways. This chapter describes the organization of SGD, the sources of the data stored in SGD, some methods for retrieving information from the database, connections SGD has with outside databases and non-yeast research communities, and SGDs repository of yeast community information.

The Gene Ontology project in 2008

The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of ‘reference’ genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface.

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over the last decade. As emphasis shifts from identification of the genes to identification of the role of their gene products in the cell, SGD seeks to provide its users with annotations that will allow relationships to be made between gene products, both within Saccharomyces cerevisiae and across species. To this end, SGD is annotating genes to the Gene Ontology (GO), a structured representation of biological knowledge that can be shared across species. The GO consists of three separate ontologies describing molecular function, biological process and cellular component. The goal is to use published information to associate each characterized S.cerevisiae gene product with one or more GO terms from each of the three ontologies. To be useful, this must be done in a manner that allows accurate associations based on experimental evidence, modifications to GO when necessary, and careful documentation of the annotations through evidence codes for given citations. Reaching this goal is an ongoing process at SGD. For information on the current progress of GO annotations at SGD and other participating databases, as well as a description of each of the three ontologies, please visit the GO Consortium page at http://www.geneontology.org. SGD gene associations to GO can be found by visiting our site at http://genome-www.stanford.edu/Saccharomyces/.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new resources that allow the comparison and integration of information on a genome-wide scale, enabling the user not only to find detailed information about individual genes, but also to make connections across groups of genes with common features and across different species. The Fungal Alignment Viewer displays alignments of sequences from multiple fungal genomes, while the Sequence Similarity Query tool displays PSI-BLAST alignments of each S.cerevisiae protein with similar proteins from any species whose sequences are contained in the non-redundant (nr) protein data set at NCBI. The Yeast Biochemical Pathways tool integrates groups of genes by their common roles in metabolism and displays the metabolic pathways in a graphical form. Finally, the Find Chromosomal Features search interface provides a versatile tool for querying multiple types of information in SGD.

Gene Ontology annotations at SGD: new data sources and annotation methods

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current.

The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now

The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called “S288C 2010,” was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.

Saccharomyces Genome Database provides mutant phenotype data

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker’s or budding yeast. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome

Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on an ongoing basis, the Saccharomyces Genome Database (SGD) () has created the Genome Snapshot (). The Genome Snapshot summarizes the current state of knowledge about the genes and chromosomal features of S.cerevisiae. The information is organized into two categories: (i) number of each type of chromosomal feature annotated in the genome and (ii) number and distribution of genes annotated to Gene Ontology terms. Detailed lists are accessible through SGDs Advanced Search tool (), and all the data presented on this page are available from the SGD ftp site ().