SRI International and European Bioinformatics Institute Significantly Expand BioCyc Collection of Pathway/Genome Databases
SRI International, an independent, nonprofit research and development organization, has significantly expanded its BioCyc collection (biocyc.org/) of pathway/genome databases to now include databases for 160 organisms. The BioCyc collection has grown from 18 to 160 organisms and now includes databases for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. The BioCyc pathway/genome databases contain information about biochemical pathways: the network of interaction between proteins and small molecules that forms the biochemical factory of a cell. Understanding these pathways is critical in the development of pharmaceuticals, which mostly operate by blocking or enhancing interactions in particular pathways. The BioCyc collection is a forum for the open sharing of this fundamental biological knowledge that will have a significant impact on the future of biology. Biomedical researchers are encouraged to adopt BioCyc databases for organisms within their expertise for refinement and further updating, and to redistribute those databases within the biomedical research community. The process is akin to the development of powerful open source software, leveraging the expertise of many to create exponential progress in the human understanding of biology. "No one group can curate all the world's genomes," said Peter Karp, Ph.D., director of SRI International's Bioinformatics Research Group. "It is imperative to involve many scientists in the updating of genome databases. Ideally, BioCyc databases are adopted, and then updated, by a group of scientists that share an interest in a specific organism or a related group of organisms." SRI collaborated with the Computational Genomics Group at the European Bioinformatics Institute (EBI), a part of the European Molecular Biology Laboratory, to add 142 new databases to the BioCyc collection. Each pathway/genome database describes the genome and predicted metabolic network of a single organism, as inferred from the related SRI MetaCyc (metacyc.org/) database of metabolic pathways from multiple organisms. BioCyc is a unique resource for researchers in genomics, bioinformatics, and systems biology that combines new information inferred from each genome with a powerful collection of query and visualization tools. "The combined use of a sophisticated software suite such as Pathway Tools from SRI and a highly curated protein database such as UniProtKB/SwissProt from the EBI has allowed the team to develop the world's most comprehensive set of pathway databases," said Christos Ouzounis, head of the Computational Genomics Group at the EBI. "BioCyc provides both breadth and depth of coverage, enabling researchers to put the vast body of data that has emerged from the genome sequencing projects into the context of what gene products are really doing in the cell. This type of work would have been unthinkable even a few years ago." To accelerate sharing of these databases once they have been adopted, SRI has established a registry of pathway/genome databases to allow scientists to register and share the databases that they curate. The adoption and database-sharing approaches will maximize the accuracy of the rapidly evolving knowledge about the genome and biochemical networks of each organism. Most BioCyc pathway/genome databases are openly available for updating and redistribution without intellectual property restrictions. Adopters can update adopted pathway/genome databases and publish them on their own Web sites, using the same Pathway Tools (bioinformatics.ai.sri.com/ptools/) software that powers the BioCyc Web site. BioCyc databases are organized into three tiers according to the degree of curation they have undergone to date. For example, the Tier 1 EcoCyc database (ecocyc.org) is a thoroughly curated encyclopedia of E. coli (Escherichia coli K12) genes and metabolism. Tier 2 pathway/genome databases have received moderate amounts of curation, whereas Tier 3 pathway/genome databases were computationally generated and received no curation. BioCyc databases exist for most of the bacteria that are the subjects of biodefense research, as well as bacteria that are being studied for use in environmental remediation and the sequestration of carbon from the atmosphere to reduce global warming. BioCyc extracts new information from each of its component genomes by predicting their metabolic pathways and, for bacteria, their operons. Scientists use the Pathway Tools Omics viewer (biocyc.org/ov-expr.shtml), available through the BioCyc Web site, to visualize combinations of gene expression, proteomics and metabolomics data on a wiring diagram for the metabolic network of a cell. The software creates animated displays of time-series omics data (a biological dataset derived from high-throughput experimentation). Large and complex omics datasets become more amenable to analyses when interpreted in the context of a cell's pathway map. The BioCyc Web site also provides a newly released genome viewer, and visualizations of operons and of individual metabolic pathways. Scientists interested in adopting a database should contact biocyc- [EMAIL PROTECTED] Most BioCyc databases are freely available to users in both commercial and non-commercial institutions. About the EBI The European Bioinformatics Institute (EBI) is part of the European Molecular Biology Laboratory (EMBL) and is located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK). The EBI grew out of EMBL's pioneering work in providing public biological databases to the research community. It hosts some of the world's most important collections of biological data, including DNA sequences (EMBL-Bank), protein sequences (UniProt), animal genomes (Ensembl), three-dimensional structures (the Macromolecular Structure Database), data from microarray experiments (ArrayExpress), protein- protein interactions (IntAct) and pathway information (Reactome). The EBI hosts several research groups and its scientists continually develop new tools for the biocomputing community. About EMBL The European Molecular Biology Laboratory is a basic research institute funded by public research monies from 18 member states (Austria, Belgium, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom). Research at EMBL is conducted by approximately 80 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and Outstations in Hinxton (the European Bioinformatics Institute), Grenoble, Hamburg, and Monterotondo near Rome. The cornerstones of EMBL's mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; and to develop new instruments and methods in the life sciences. EMBL's International PhD Programme has a student body of about 170. The Laboratory also sponsors an active Science and Society programme. Visitors from the press and public are welcome. About SRI International Silicon Valley-based SRI International (www.sri.com) is one of the world's leading independent research and technology development organizations. Founded as Stanford Research Institute in 1946, SRI has been meeting the strategic needs of clients for almost 60 years. The nonprofit research institute performs contract research and development for government agencies, commercial businesses and nonprofit foundations. 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