title: Updates in Rhea--a manually curated resource of biochemical reactions.
abstract: Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models.
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Genoscope-LABGeM, CEA, Evry, F-91057, France anne.morgat@isb-sib.ch.
authors.forename: Anne
authors.initials: A
authors.lastname: Morgat
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Kristian B
authors.initials: KB
authors.lastname: Axelsen
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Thierry
authors.initials: T
authors.lastname: Lombardot
authors.affiliation: Equipe BAMBOO, INRIA Grenoble Rhône-Alpes, Montbonnot Saint-Martin, F-38330, France.
authors.forename: Rafael
authors.initials: R
authors.lastname: Alcántara
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Lucila
authors.initials: L
authors.lastname: Aimo
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Zerara
authors.affiliation: Cheminformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, CB10 1SD, UK.
authors.forename: Anne
authors.initials: A
authors.lastname: Niknejad
authors.affiliation: Department of Biochemistry, University of Geneva, Geneva, CH-1206, Switzerland.
authors.forename: Eugeni
authors.initials: E
authors.lastname: Belda
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Nevila
authors.initials: N
authors.lastname: Hyka-Nouspikel
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Coudert
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Nicole
authors.initials: N
authors.lastname: Redaschi
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Lydie
authors.initials: L
authors.lastname: Bougueleret
authors.affiliation: Equipe BAMBOO, INRIA Grenoble Rhône-Alpes, Montbonnot Saint-Martin, F-38330, France.
authors.forename: Christoph
authors.initials: C
authors.lastname: Steinbeck
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Cheminformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, CB10 1SD, UK.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Alan
authors.initials: A
authors.lastname: Bridge
mesh_terms: D001669:Biochemical Phenomena; D001704:Biopolymers / Q000378:metabolism; D062126:Databases, Chemical; D004798:Enzymes / Q000378:metabolism*; D023281:Genomics; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics
chemical_list: D001704:Biopolymers; D004798:Enzymes