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Nucleic Acids Res. 2015 Jan;43(Database issue):D459-64. doi: 10.1093/nar/gku961. Epub 2014 Oct 20.

Updates in Rhea--a manually curated resource of biochemical reactions.

Author information

1
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Genoscope-LABGeM, CEA, Evry, F-91057, France anne.morgat@isb-sib.ch.
2
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
3
Equipe BAMBOO, INRIA Grenoble Rhône-Alpes, Montbonnot Saint-Martin, F-38330, France.
4
Cheminformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, CB10 1SD, UK.
5
Department of Biochemistry, University of Geneva, Geneva, CH-1206, Switzerland.
6
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Cheminformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, CB10 1SD, UK.

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.

PMID:
25332395
PMCID:
PMC4384025
DOI:
10.1093/nar/gku961
[Indexed for MEDLINE]
Free PMC Article

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