title: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
abstract: The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.
authors.affiliation: Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA. pkarp@ai.sri.com
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: Christos A
authors.initials: CA
authors.lastname: Ouzounis
authors.forename: Caroline
authors.initials: C
authors.lastname: Moore-Kochlacs
authors.forename: Leon
authors.initials: L
authors.lastname: Goldovsky
authors.forename: Pallavi
authors.initials: P
authors.lastname: Kaipa
authors.forename: Dag
authors.initials: D
authors.lastname: Ahrén
authors.forename: Sophia
authors.initials: S
authors.lastname: Tsoka
authors.forename: Nikos
authors.initials: N
authors.lastname: Darzentas
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Núria
authors.initials: N
authors.lastname: López-Bigas
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D016678:Genome; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D008660:Metabolism / Q000235:genetics