Updates in Rhea-a manually curated resource of biochemical reactions

Anne Morgat (1, 2, 3) , Kristian B. Axelsen (1) , Thierry Lombardot (1) , Rafael Alcantara (4) , Lucila Aimo (1) , Mohamed Zerara (1) , Anne Niknejad (5) , Eugéni Belda (6) , Nevila Hyka-Nouspikel (1) , Elisabeth Coudert (1) , Nicole Redaschi (1) , Lydie Bougueleret (1) , Christoph Steinbeck (4) , Ioannis Xenarios (1, 5) , Alan Bridge (1)

1 Swiss-Prot Group
2 LABGeM - Analyse Bio-Informatique pour la Génomique et le Métabolisme
3 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
4 BAMBOO - An algorithmic view on genomes, cells, and environments
5 EMBL-EBI - European Bioinformatics Institute [Hinxton]
6 UNIGE - Université de Genève = University of Geneva

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.

Domains: Genetics

Anne Morgat, Kristian B. Axelsen, Thierry Lombardot, Rafael Alcantara, Lucila Aimo, et al.. Updates in Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Research, 2015, 43 (D1), pp.D459-D464. ⟨10.1093/nar/gku961⟩. ⟨cea-04573296⟩