Mike Cherry

Research/Lab website:   Saccharomyces Genome Database

Dr. Cherry's lab develops and maintains the Saccharomyces Genome Database (SGD; www.yeastgenome.org). This NIH National Genome Research Resource Center, a public Web resource, provides information and tools on budding yeast genome, its products and their interactions. His group is ever expanding SGD to capture the new results from functional genomics, the systematic study of the processes that occur within this organism, and the results of published classical genetics plus molecular and cellular biology. The genomic sequence, functional genomic and published literature information is combined in a meaningful manner that allow biologist to explore this encyclopedic database. SGD allows four primary methods of entry for browsing. These entry points allow users to select a gene knowing its name, DNA or protein sequence, literature keywords, or its role/function within the cell. In addition, several computational tools have been developed to provide to allow the research community to explore the collected data sets. Tools for querying >50,000 full-text papers are also provided. SGD has become an essential research tool used daily by thousands of researchers around the globe.

The second area of research is in the creation of ontologies to aid communication between biologists as well as biological database projects. His group is a founding member of the Gene Ontology (GO) Collaboration. The GO project, originally conceived by Prof. Michael Ashburner at the University of Cambridge, is a collaboration between many genome databases including: FlyBase (Drosophila), Mouse Genome Informatics (Mus), The Arabidopsis Information Resource (Arabidopsis), WormBase (Caenorhabditis), ZFin (Danio), Rat Genome Database (Rattus), dictyBase (Dictyostilium), PomBase (Schizosaccharomyces), and SGD (Saccharomyces). There are many hierarchical classification systems for protein function, protein secondary structure and protein families. These classifications are very useful, however they were not designed to describe the higher-level biological roles gene products play within the cell. The GO collaboration is developing three independent ontologies that are used for gene product annotation (www.GeneOntology.org). The three ontologies are Biological Process, Molecular Function and Cellular Component. These ontologies provide a controlled vocabulary that is significant in the unification of biological terms. The defined phrases, often called GO terms, have been used to annotate all yeast genes that have phenotype, localization or functional information from the published literature. The ontologies allow specific linkage between the member databases of the collaboration. As members of the consortium we are developing the terms (including a definition for each term), plus databases and software for the many uses of the ontologies. Dr. Cherry’s group provides the production computing environment for the GO via a variety of Internet resources.