Updates in Rhea – an expert curated resource of biochemical reactions

Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research. These include the first implementation of a simple hierarchical classification of reactions, improved coverage of the IUBMB Enzyme Nomenclature list and additional reactions through continuing expert curation, and the development of a new website to serve this improved dataset.

[1]  Gemma L. Holliday,et al.  EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions , 2014, Nature Methods.

[2]  Arthur Dalby,et al.  Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited , 1992, J. Chem. Inf. Comput. Sci..

[3]  H. Fyrst,et al.  Sphingosine Phosphate Lyase Expression Is Essential for Normal Development in Caenorhabditis elegans* , 2003, Journal of Biological Chemistry.

[4]  Christoph Steinbeck,et al.  The EBI enzyme portal , 2012, Nucleic Acids Res..

[5]  Andrew G McDonald,et al.  Fifty‐five years of enzyme classification: advances and difficulties , 2014, The FEBS journal.

[6]  Alan Bridge,et al.  The SwissLipids knowledgebase for lipid biology , 2015, Bioinform..

[7]  Thomas Bernard,et al.  Reconciliation of metabolites and biochemical reactions for metabolic networks , 2012, Briefings Bioinform..

[8]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions , 2006, J. Chem. Inf. Model..

[9]  Christoph Steinbeck,et al.  MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data , 2012, Nucleic Acids Res..

[10]  Rolf Apweiler,et al.  IntEnz, the integrated relational enzyme database , 2004, Nucleic Acids Res..

[11]  Andrew G. McDonald,et al.  ExplorEnz: the primary source of the IUBMB enzyme list , 2008, Nucleic Acids Res..

[12]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[13]  Christoph Steinbeck,et al.  Reaction Decoder Tool (RDT): extracting features from chemical reactions , 2016, Bioinform..

[14]  Christoph Steinbeck,et al.  Rhea—a manually curated resource of biochemical reactions , 2011, Nucleic Acids Res..

[15]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[16]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[17]  V. Gupta,et al.  Sphingosine-phosphate Lyase Enhances Stress-induced Ceramide Generation and Apoptosis* , 2004, Journal of Biological Chemistry.

[18]  Christoph Steinbeck,et al.  Updates in Rhea—a manually curated resource of biochemical reactions , 2014, Nucleic Acids Res..

[19]  Christoph Steinbeck,et al.  ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..

[20]  O. Cuvillier,et al.  First Evidence of Sphingosine 1-Phosphate Lyase Protein Expression and Activity Downregulation in Human Neoplasm: Implication for Resistance to Therapeutics in Prostate Cancer , 2012, Molecular Cancer Therapeutics.

[21]  Stefan Engelen,et al.  MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data , 2012, Nucleic Acids Res..

[22]  Gary D Bader,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[23]  Tae Yong Kim,et al.  RxnSim: a tool to compare biochemical reactions , 2015, Bioinform..

[24]  Olivier Martin,et al.  MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks , 2015, Nucleic Acids Res..

[25]  Suzanna Lewis,et al.  Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium , 2011, Briefings Bioinform..