Saccharomyces Genome Database

Saccharomyces Genome Database
Name	Saccharomyces Genome Database
Type	Biological database
Established	1993
Country	United States
Institution	Stanford University

Saccharomyces Genome Database The Saccharomyces Genome Database provides comprehensive genetic and molecular information about the yeast species Baker's yeast, curated sequence data, functional annotation, and tools for analysis. It supports researchers working with Saccharomyces cerevisiae, links to model organism resources such as FlyBase, WormBase, Mouse Genome Informatics, and integrates literature from publishers like Nature (journal), Science (journal), and Proceedings of the National Academy of Sciences.

Overview

The database centralizes annotated genome sequence, gene models, and functional data for the model organism Saccharomyces cerevisiae, connecting genotype to phenotype for users from labs at Stanford University, Harvard University, Massachusetts Institute of Technology, and international centers like European Bioinformatics Institute and Japan Biological Informatics Consortium. It provides cross-references to external resources including UniProt, Gene Ontology Consortium, NCBI, Ensembl, KEGG, Reactome, Protein Data Bank, ArrayExpress, GEO, EMBL-EBI, Broad Institute, Wellcome Sanger Institute, Max Planck Society, Cold Spring Harbor Laboratory, Howard Hughes Medical Institute, Karolinska Institutet, University of Tokyo, Chinese Academy of Sciences, European Molecular Biology Laboratory, Institut Pasteur, Monash University, University of Cambridge, and University of Oxford.

History and Development

Originally initiated in the early 1990s to support the Saccharomyces cerevisiae genome sequencing project coordinated by groups at Whitehead Institute, Genolevures Consortium, and the Sanger Centre, the database evolved through collaborations with principal investigators at Stanford University and curators trained at institutions like Cold Spring Harbor Laboratory and European Bioinformatics Institute. Key milestones included integration of curated literature from journals such as Cell (journal), inclusion of functional annotation standards from the Gene Ontology Consortium, adoption of data interchange formats used by RefSeq, and participation in community initiatives like the International Yeast Community and projects supported by funders such as the National Institutes of Health, European Research Council, and Wellcome Trust.

Data Content and Curation

Content includes genome sequence, open reading frame annotations, regulatory elements, phenotype annotations, genetic interactions, protein complexes, and curated literature notes drawn from articles in Genetics (journal), Molecular and Cellular Biology, EMBO Journal, Genome Research, and conference proceedings of the Yeast Genetics Meeting and European Yeast Conference. Curators reconcile evidence from experimental work at labs led by investigators such as those affiliated with Harvard Medical School, University of California, San Diego, Yale University, University of Chicago, and repositories like BioGRID, IntAct, STRING, PDB, and PhosphoSitePlus to assign standardized terms from resources including the Gene Ontology Consortium, Sequence Ontology, Chemical Entities of Biological Interest, and Human Phenotype Ontology.

Tools and Services

The platform provides search and download utilities, genome browsers compatible with tracks from UCSC Genome Browser, sequence alignment and BLAST services interoperable with NCBI BLAST, batch query tools similar to Ensembl BioMart, and visualization modules inspired by interfaces at Cytoscape and JBrowse. Analytical services support pathway mapping using KEGG and Reactome integrations, network analyses leveraging Cytoscape plugins, and comparative genomics workflows that relate yeast genes to orthologs from projects at Broad Institute, Ensembl Genomes, and annotations in UniProtKB.

Access and Community Contributions

The database is freely accessible to academic and nonprofit users, with data downloads patterned after archives such as GenBank and submission pipelines compatible with standards from INSDC and citation practices reflecting journals like Nature Genetics and Genome Biology. Community contribution pipelines accept curated submissions, annotations, and phenotype reports from researchers at institutions such as University of Toronto, University of Melbourne, Seoul National University, and community consortia like the International Nucleotide Sequence Database Collaboration; contributors are credited per policies similar to those of Open Science Framework and funding acknowledgements follow guidance from National Science Foundation and National Institutes of Health.

Impact and Applications

The resource underpins research in cell biology, genetics, systems biology, and biotechnology, informing studies published in Nature, Science, Cell (journal), and applied work in industrial settings like breweries associated with Anheuser-Busch and biotech firms collaborating with Genentech and Novozymes. It has enabled discoveries in pathways conserved in Homo sapiens and translational studies at institutions such as Broad Institute and Massachusetts General Hospital, supported education in university courses at Stanford University and MIT, and serves as a model for organism-specific databases alongside FlyBase, WormBase, and Mouse Genome Informatics.

Category:Biological databases