Database Commons

a catalog of worldwide biological databases

The Yeast Proteome Database (YPD) is a model for the organization and presentation of comprehensive protein information. Based on the detailed curation of the scientific literature for the yeast Saccharomyces cerevisiae, YPD contains more than 50 000 annotations lines derived from the review of 8500 research publications. The information concerning each of the approximately 6100 yeast proteins is structured around a convenient one-page format, the Yeast Protein Report, with additional information provided as pop-up windows. Protein classification schema have been revised this year, defining each protein's cellular role, function and pathway, and adding a Functional to the Yeast Protein Report. These changes provide the user with a succinct summary of the protein's function and its place in the biology of the cell, and they enhance the power of YPD Search functions. Precalculated sequence alignments have been added, to provide a crossover point for comparative genomics. The first transcript profiling data has been integrated into the YPD Protein Reports, providing the framework for the presentation of genome-wide functional data. The Yeast Proteome Database can be accessed on the Web at http://www.proteome.com/YPDhome.html

The Yeast Protein Database (YPD) is a curated database for the proteome of Saccharomyces cerevisiae . It consists of approximately 6000 Yeast Protein Reports, one for each of the known or predicted yeast proteins. Each Yeast Protein Report is a one-page presentation of protein properties, annotation lines that summarize findings from the literature, and references. In the past year, the number of annotation lines has grown from 25 000 to approximately 35 000, and the number of articles curated has grown from approximately 3500 to >5000. Recently, new data types have been included in YPD: protein-protein interactions, genetic interactions, and regulators of gene expression. Finally, a new layer of information, the YPD Protein Minireviews, has recently been introduced. The Yeast Protein Database can be found on the Web at http://www.proteome.com/YPDhome. html

The Yeast Protein Database (YPD) is a database for the proteins of the budding yeast,Saccharomyces cerevisiae. YPD is the first annotated database for the complete proteome of any organism. Now that the complete genome sequence of yeast is available, YPD contains entries for each of the characterized proteins and for each of the uncharacterized proteins predicted from the sequence. Contained in YPD are the calculated properties of each protein such as molecular weight and isoelectric point, experimentally determined properties such as subcellular localization and post-translational modifications, and extensive annotations from the yeast literature. YPD contains 25 000 lines of textual annotation that describe the known functions, mutant phenotypes, interactions, and other properties for the approximately 6000 proteins in the yeast proteome. The information in YPD is updated daily, and it is available on the World Wide Web at http://www.proteome.com/YPDhome.html .