Joan E. Brooks

The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information

The Yeast Proteome Database (YPDtrade mark) has been for several years a resource for organized and accessible information about the proteins of Saccharomyces cerevisiae. We have now extended the YPD format to create a database containing complete proteome information about the model organism Caenorhabditis elegans (WormPDtrade mark). YPD and WormPD are designed for use not only by their respective research communities but also by the broader scientific community. In both databases, information gleaned from the literature is presented in a consistent, user-friendly Protein Report format: a single Web page presenting all available knowledge about a particular protein. Each Protein Report begins with a Title Line, a concise description of the function of that protein that is continually updated as curators review new literature. Properties and functions of the protein are presented in tabular form in the upper part of the Report, and free-text annotations organized by topic are presented in the lower part. Each Protein Report ends with a comprehensive reference list whose entries are linked to their MEDLINE s. YPD and WormPD are seamlessly integrated, with extensive links between the species. They are freely accessible to academic users on the WWW at http://www. proteome.com/databases/index.html, and are available by subscription to corporate users.

Three yeast proteome databases: YPD, pombePD, and CalPD (MycopathPD)

Publisher Summary Proteomes fungal databases, YPD (for Saccharomyces cerevisiae), PombePD (for Schizosaccharomyces pombe), and CalPD (for Candida albicans), work together to present a comprehensive view of the molecular and cell biology of the genes and proteins of the fungal world. YPD, CalPD, and PombePD are part of a group of databases collectively called the BioKnowledge Library, which also includes databases for complex organisms, such as the worm Caenorhabditis elegans (WormPD), a model for development of a multicellular organism, and a protein survey database for humans. This chapter we provide detailed coverage of the YPD database, which has served as the prototype for the creation of all other volumes of the BioKnowledge Library. The chapter presents the unique features of the newer fungal databases PombePD and CalPD. CalPD is expected to be incorporated into MycoPathPD, a new volume that will include genes and proteins of C. albicans and other human pathogenic fungi. YPD is recommended as a good initiation site for newcomers.