title: Computational Metabolomics Operations at BioCyc.org.
abstract: BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a "universal" metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services.
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. billingt@ai.sri.com.
authors.forename: Richard
authors.initials: R
authors.lastname: Billington
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. timothy.holland@sri.com.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Holland
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. kothari@ai.sri.com.
authors.forename: Anamika
authors.initials: A
authors.lastname: Kothari
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. kr@ai.sri.com.
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. weaver@ai.sri.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: Weaver
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. latendre@ai.sri.com.
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. paley@ai.sri.com.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
keywords: metabolic database; metabolic pathways; metabolomics data analysis